(1973). "Enterovirus recovery with vegetable floc." Appl Microbiol 26(4): 505-7.
	
(1997). "Viral gastroenteritis associated with eating oysters -- Louisiana, December 1996-January 1997." MMWR Morb Mortal Wkly Rep 46(47): 1109-12.
	Viral gastroenteritis outbreaks caused by caliciviruses (i.e., Norwalk-like viruses or small round-structured viruses) have been associated with eating contaminated shellfish, particularly oysters (Crassostrea virginica). This report describes the findings of the investigation of an outbreak of oyster-associated viral gastroenteritis in Louisiana during the 1996-97 winter season and implicates sewage from oyster harvesting vessels as the probable cause of contaminated oysters.

(2000). "Foodborne outbreak of Group A rotavirus gastroenteritis among college students--District of Columbia, March-April 2000." MMWR Morb Mortal Wkly Rep 49(50): 1131-3.
	On March 31, student health services at a university in the District of Columbia (DC) notified the DC health department that an increased number of students had become ill with acute gastroenteritis beginning March 29. Some ill students reported eating tuna or chicken salad sandwiches from dining hall A on campus. On March 31, the DC health department initiated an outbreak investigation. This report summarizes results of the investigation, which indicated that group A rotavirus transmitted by food was the cause of the outbreak.

(2001). "From the Centers for Disease Control and Prevention. Foodborne outbreak of group A rotavirus gastroenteritis among college students--District of Columbia, March-April 2000." Jama 285(4): 405-6.
	
(2002). "From the Centers for Disease Control and Prevention. Outbreak of acute gastroenteritis associated with Norwalk-like viruses among British military personnel--Afghanistan, May 2002." Jama 287(24): 3203-4.
	
(2002). "From the Centers for Disease Control and Prevention. Possible West Nile virus transmission to an infant through breast-feeding--Michigan, 2002." Jama 288(16): 1976-7.
	
(California), S. D. o. H. S. (1981). "Hepatitis A outbreak associated with a food handler - Los Angeles." California Morbidity Weekly Report 39: 1.
	
Abad, F. X., R. M. Pinto, et al. (1994). "Survival of enteric viruses on environmental fomites." Appl Environ Microbiol 60(10): 3704-10.
	The survival of human enteric viruses on several porous (paper and cotton cloth) and nonporous (aluminum, china, glazed tile, latex, and polystyrene) environmental surfaces has been evaluated. Viruses persisted for extended periods on several types of materials commonly found in institutions and domestic environments. The stability of the viruses was generally influenced by environmental factors such as relative humidity (RH), temperature, and the type of surface contaminated. Overall, hepatitis A virus (HAV) and human rotavirus (HRV) were more resistant to inactivation than enteric adenovirus (ADV) and poliovirus (PV). The resistance to the desiccation step appears to be of major significance in determining the survival of a virus dried on fomites. ADV and PV showed a pronounced decrease in titer at this stage, whereas HAV and HRV displayed little decay at the desiccation step. HAV and HRV persistence was not affected by the presence of fecal material. On nonporous surfaces, PV and ADV persisted better in the presence of feces. However, on porous fomites the presence of fecal material had a negative influence on the survival of PV and ADV. Except for HRV, greater virus survival was observed at 4 degrees than at 20 degrees C. PV and HAV survival was enhanced at high RH; the survival of the latter was enhanced at least for nonporous materials. When dried on porous materials, HRV also exhibited greater persistence at high RH. The survival of ADV was not affected by RH. The validity of using bacteriophages of Bacteroides fragilis as indicators of human viruses dried on fomites was evaluated.(ABSTRACT TRUNCATED AT 250 WORDS)

Abad, F. X., R. M. Pinto, et al. (1997). "Disinfection of human enteric viruses on fomites." FEMS Microbiol Lett 156(1): 107-11.
	The virucidal action of several commercially available disinfectant preparations was assayed against hepatitis A virus and human rotavirus dried on polystyrene. Overall, the level of virus disinfection achieved was very poor, usually inducing less than 3 log titre reduction. Suspension tests performed with the same disinfectants showed different virus inactivation rates, thus failing to provide a reliable indication of the actual virus disinfection on fomites. In our studies, bacteriophages of Bacteroides fragilis proved to be a simple, cheap and reliable screening tool for the evaluation of virus disinfection on non-porous surfaces. The same conclusion cannot be drawn for poliovirus.

Abad, F. X., R. M. Pinto, et al. (1998). "Flow cytometry detection of infectious rotaviruses in environmental and clinical samples." Appl Environ Microbiol 64(7): 2392-6.
	A method for the detection of infectious human rotaviruses based on infection of CaCo-2 cells and detection of infected cells by indirect immunofluorescence and flow cytometry (IIF-FC) has been developed. The technique was validated by performing a seminested reverse transcription-PCR assay with sorted cell populations. The efficiency of the procedure has been compared with that of the standard method of infection of MA104 cells and ulterior detection by IIF and optical microscopy (IIF-OM) and with that of infection of MA104 cells and detection by IIF-FC. The limit of sensitivity for the detection of the cell-adapted strain Ito(r) P13, expressed as the most probable number of cytopathogenic units, was established as 200 and 2 for MA104 and CaCo-2 cells, respectively, by the IIF-FC method. The ratio of infectious virus particles to total virus particles for a wild-type rotavirus was determined to be 1/2 x 10(6) and 1/2 x 10(4) for IIF-OM with MA104 cells and IIF-FC with CaCo-2 cells, respectively. The use of IIF-FC with CaCo-2 cells was tested with fecal and water samples and proved to be more effective than the standard procedure for rotavirus detection.

Abad, F. X., R. M. Pinto, et al. (1994). "Disinfection of human enteric viruses in water by copper and silver in combination with low levels of chlorine." Appl Environ Microbiol 60(7): 2377-83.
	The efficacy of copper and silver ions, in combination with low levels of free chlorine (FC), was evaluated for the disinfection of hepatitis A virus (HAV), human rotavirus (HRV), human adenovirus, and poliovirus (PV) in water. HAV and HRV showed little inactivation in all conditions. PV showed more than a 4 log10 titer reduction in the presence of copper and silver combined with 0.5 mg of FC per liter or in the presence of 1 mg of FC per liter alone. Human adenovirus persisted longer than PV with the same treatments, although it persisted significantly less than HRV or HAV. The addition of 700 micrograms of copper and 70 micrograms of silver per liter did not enhance the inactivation rates after the exposure to 0.5 or 0.2 mg of FC per liter, although on some occasions it produced a level of inactivation similar to that induced by a higher dose of FC alone. Virus aggregates were observed in the presence of copper and silver ions, although not in the presence of FC alone. Our data indicate that the use of copper and silver ions in water systems may not provide a reliable alternative to high levels of FC for the disinfection of viral pathogens. Gene probe-based procedures were not adequate to monitor the presence of infectious HAV after disinfection. PV does not appear to be an adequate model viral strain to be used in disinfection studies. Bacteroides fragilis bacteriophages were consistently more resistant to disinfection than PV, suggesting that they would be more suitable indicators, although they survived significantly less than HAV or HRV.

Abad, F. X., R. M. Pinto, et al. (1997). "Viruses in mussels: Public health implications and depuration." Journal of Food Protection 60(6): 677-681.
	Studies were conducted in the common musset (Mytilus spp.) to evaluate the public health implications derived from shellfish contamination with human pathogenic enteric viruses. In bioaccumulation experiments, we could verify that after 6 h of immersion of mussels in marine water contaminated with high levels of clay-associated enteric adenovirus (type 40) and human rotavirus (type 3), between 4 to 56% of the seeded viruses were adsorbed to shellfish tissues, mainly in the gills and digestive tract. We investigated the occurrence of wild-type enteric viruses in mussels from sites with different levels of fecal pollution. Pathogenic viruses could be detected in mussels from areas that, following current standards based on bacteriological quality, should be regarded as unpolluted, safe for swimming, and suitable for harvesting shellfish. Cooking experiments performed with contaminated mussels revealed that 5 min after the opening of the mussel valves, rotaviruses and hepatitis A virus could still be recovered in steamed shellfish. Under commercial depuration conditions, health-significant enteric viruses, such as rotavirus and hepatitis A virus, could be recovered from bivalves after 96 h of immersion in a continuous how of ozonated marine water. Routine screening of bivalves for the presence of health-significant enteric viruses before public consumption may help in the prevention of outbreaks among shellfish consumers.

Abad, F. X., R. M. Pinto, et al. (1997). "Astrovirus survival in drinking water." Appl Environ Microbiol 63(8): 3119-22.
	A method based on infection of CaCo-2 cultured cell monolayers (CC) and reverse transcription-PCR (RT-PCR) was developed for the specific detection of infectious astrovirus. The procedure was validated by titrating poliovirus stocks in parallel in CaCo-2 cells by determining the most probable number of cytopathogenic units and by cell culture and subsequent RT-PCR (CC-RT-PCR). CC-RT-PCR was then employed to measure the persistence of astrovirus suspended in dechlorinated tap water. After 60 days, the decay of astrovirus infectivity was 2 log units at 4 +/- 1 degrees C and 3.2 log units at 20 +/- 1 degrees C, while after 90 days, the titer reduction was 3.3 and 5 log units at 4 +/- 1 degrees C and 20 +/- 1 degrees C, respectively. Astrovirus decay in the presence of free chlorine (FC) was monitored by CC-RT-PCR. Residual infectivity was found after 2 h in the presence of 1 mg of FC/liter. Under these conditions, astrovirus shows a log titer reduction (LTR) or 4, while 0.5 mg of FC/liter induced an LTR of 2.4. The possibility of acquiring data on the survival of fastidious viruses in the environment opens new perspectives on the epidemiology of some significant infections transmitted by the fecal-oral route.

Abad, F. X., C. Villena, et al. (2001). "Potential role of fomites in the vehicular transmission of human astroviruses." Appl. Environ. Microbiol. 67(9): 3904-3907.
	The persistence of human astroviruses dried on representative porous (paper) and nonporous (china) surfaces was investigated. Long-term astrovirus survival on fomites was monitored by an integrated cell culture-reverse transcription-PCR procedure. Viruses were applied to inanimate surfaces in the presence and absence of fecal material, and their survival was assayed at 4 and 20 degrees C with high relative humidity. Astroviruses exhibited a notable persistence when dried on porous and nonporous materials, particularly at low temperature. Short-term survival of astroviruses on fomites was compared to that of other enteric viruses significant for health, such as rotavirus, adenovirus, poliovirus, and hepatitis A virus. Overall, astroviruses persisted better than poliovirus and adenovirus, although they exhibited a shorter survival than rotavirus and hepatitis A virus. Astroviruses show a high level of persistence at the desiccation step, which is of major significance in determining the chance of subsequent virus survival dried on fomites. Astroviruses are able to survive on inert surfaces long enough to suggest that fomites may play a relevant role in the secondary transmission of astrovirus diarrhea.

Abbaszadegan, M. (1993). Evaluation of the disinfection efficiency of a point-of-use water treatment system on protozoan, viral, and bacterial pathogens. Water Quality Technology Conference, Toronto, Ontario, Canada, Denver, CO : American Water Works Association, 1993.
	
Abbaszadegan, M., M. S. Huber, et al. (1993). "Detection of enteroviruses in groundwater with the polymerase chain reaction." Applied and Environmental Microbiology 59(5): 1318-1324.
	Standard methods for the detection of enteroviruses in environmental samples involve the use of cell culture, which is expensive and time-consuming. The polymerase chain reaction (PCR) is an attractive method for the detection of enteroviruses in water because primary cell culture is not needed and the increased sensitivity of PCR allows detection of the low numbers of target DNAs and RNAs usually found in environmental samples. However, environmental samples often contain substances that inhibit PCR amplification of target DNA and RNA. Procedures that remove substances that interfere with the amplification process need to be developed if PCR is to be successfully applied to environmental samples. An RNA-PCR assay for the detection of enteroviruses in water was developed and used to test a variety of groundwater concentrates and humic acid solutions seeded with poliovirus type 1. The groundwater samples and humic acid solutions were treated with Sephadex G-50, Sephadex G-100, Sephadex G-200, Chelex-100 resin, and a mixed bed resin to remove PCR-inhibitory material from the samples. Sephadex G-100 in combination with Chelex-100 was found to be very effective in removing inhibitory factors for the detection of enteroviruses in groundwater concentrates by PCR. Viruses were detected in two of the groundwater concentrates by the RNA-PCR assay after treatment with Sephadex G-100 plus Chelex-100. This was confirmed by tissue culture, suggesting that the treatment protocol and, subsequently, the RNA-PCR assay are applicable for the detection of enteroviruses in environmental samples. 

Abbaszadegan, M., P. Stewart, et al. (1999). "A strategy for detection of viruses in groundwater by PCR." Applied and Environmental Microbiology 65(2): 444-449.
	We evaluated the use of the PCR for detection of enteric viruses in groundwater. To do this, we used an improved sample-processing technique and a large-volume amplification protocol. The objective of this study was to use advanced molecular techniques to develop a rapid and simple method which can be used by the water industry for detection of viral contamination in a variety of water samples. The strategy described here fulfills the water industry's need for a rapid, reliable, easily performed method for analyzing groundwater for virus contamination. Viruses were detected after concentration from at least 400 gallons (1,512 liters) of water by a filter adsorption and elution method, which resulted in a concentrate containing viruses. A total of 150 samples were analyzed by performing cell culture assays for enteroviruses and by performing reverse transcription PCR (RT-PCR) analyses for enteroviruses, hepatitis A virus, and rotavirus. Thirteen samples (8.7%) produced cellular cytopathic effects when the Buffalo green monkey cell line was used. When primers specific for enteroviruses were used in RT-PCR, 40 of 133 samples (30.1%) tested positive for the presence of enterovirus RNA. When hepatitis A virus-specific primers were used, 12 of 139 samples (8.6%) were considered positive for the presence of hepatitis A viral RNA. The RT-PCR analysis performed with rotavirus-specific primers identified 18 of 130 samples (13.8%) that were positive for rotavirus RNA sequences. Our sample-processing technique and large-volume PCR protocol (reaction volume, 300 microliter) resulted in sufficient removal or dilution of inhibitors so that more than 95% of the samples could be assayed by PCR. Because of its sensitivity for detecting viral nucleic acid sequences, PCR analysis should produce more positive results than cell culture analysis. Since either cell culture analysis or PCR can reveal only a "snapshot" of the quality of the groundwater being sampled, PCR seems to be a desirable rapid initial screening tool. 

Abbaszadegan, M., P. W. Stewart, et al. (2003). "Occurrence of viruses in US groundwaters." J. Am. Water Works Assoc. 95: 107-120.
	
Abd El Galil, K. H., M. A. El Sokkary, et al. (2004). "Combined immunomagnetic separation-molecular beacon-reverse transcription-PCR assay for detection of hepatitis A virus from environmental samples." Appl Environ Microbiol 70(7): 4371-4.
	In this study, a molecular-beacon-based real-time reverse transcription (RT)-PCR assay was developed to detect the presence of hepatitis A virus (HAV) in environmental samples. A 125-bp, highly conserved 5' noncoding region of HAV was targeted. The sensitivity of the real-time RT-PCR assay was tested with 10-fold dilutions of viral RNA, and a detection limit of 1 PFU was obtained. The specificity of the assay was demonstrated by testing with other environmental pathogens and indicator microorganisms, and only HAV was positively identified. When combined with immunomagnetic separation, the real-time RT-PCR assay successfully detected as few as 20 PFU in seeded groundwater samples. Because of its simplicity and specificity, this assay has broad applications for the rapid detection of HAV in contaminated foods or water.

Abd el-Galil, K. H., M. A. el-Sokkary, et al. (2005). "Real-time nucleic acid sequence-based amplification assay for detection of hepatitis A virus." Appl Environ Microbiol 71(11): 7113-6.
	A nucleic acid sequence-based amplification (NASBA) assay in combination with a molecular beacon was developed for the real-time detection and quantification of hepatitis A virus (HAV). A 202-bp, highly conserved 5' noncoding region of HAV was targeted. The sensitivity of the real-time NASBA assay was tested with 10-fold dilutions of viral RNA, and a detection limit of 1 PFU was obtained. The specificity of the assay was demonstrated by testing with other environmental pathogens and indicator microorganisms, with only HAV positively identified. When combined with immunomagnetic separation, the NASBA assay successfully detected as few as 10 PFU from seeded lake water samples. Due to its isothermal nature, its speed, and its similar sensitivity compared to the real-time RT-PCR assay, this newly reported real-time NASBA method will have broad applications for the rapid detection of HAV in contaminated food or water.

Aberham, C., C. Pendl, et al. (2001). "A quantitative, internally controlled real-time PCR Assay for the detection of parvovirus B19 DNA." J Virol Methods 92(2): 183-91.
	Parvovirus B19 is an erythrovirus causing diverse clinical manifestations ranging from asymptomatic or mild, to more severe outcomes in, for example, immune-compromised patients. B19 is spread primarily via the respiratory route, but it can also be transmitted via blood and blood products. Viral loads in blood or plasma donations amount up to 10(11) genome equivalents/ml. Therefore, screening of plasma for fractionation for the presence of B19 and removal of highly loaded donations is a way to limit considerably the input of B19 into production pools and to improve further the safety of plasma products.An assay for the quantitative detection of B19 DNA, based on real-time PCR using ABI Prism SDS7700 (TaqMan) is described here. This assay allows precise quantitation of viral loads over 7 orders of magnitude. An exogenous internal control (internal quality marker) is included in each individual sample to prevent false negative results. A linearized plasmid is used as an internal quality marker that contains the identical sequence of the B19 target sequence but with an altered probe hybridization site. This allows co-amplification of B19 and internal quality marker and co-detection of FAM (6-carboxyfluorescein) or VIC labeled probes respectively. The assay is validated according to current guidelines (of the International Conference on Harmonization, Paul Ehrlich Institute, and the Council of Europe) and is optimized for high throughput screening.

Abolmaaty, A., W. Gu, et al. (2007). "The use of activated charcoal for the removal of PCR inhibitors from oyster samples." J Microbiol Methods 68(2): 349-52.
	Activated charcoal is a carbonaceous adsorbent with a high internal porosity, and hence a large internal surface area. Cells of a strain of Escherichia coli O157:H7 seeded into oyster tissue homogenates were completely bound to untreated charcoal after an incubation period of 15 min at room temperature. In contrast, activated charcoal particles coated with cells of Pseudomonas fluorescens resulted in 92.6%+/-3.7 recovery of E. coli O157:H7. This allowed the successful use of the coated activated charcoal for the absorption of PCR inhibitors from seeded tissue samples. With coated charcoal, real-time PCR was able to detect 1x10(3) CFU of E. coli 0157:H7/g of tissue which was equivalent to 50 genomic targets per real-time PCR. In contrast, without the use of treated charcoal, the real-time PCR failed to detect 10(7) CFU/g. This is a promising, and convenient technology that can be applied to increase the sensitivity of the PCR assay without selective enrichment, for the detection of low numbers of pathogenic microorganisms in complex matrices such as foods, clinical, and environmental samples, which frequently exhibit high levels of PCR inhibition.

Abraham, R., T. Chonmaitree, et al. (1993). "Rapid detection of poliovirus by reverse transcription and polymerase chain amplification: application for differentiation between poliovirus and nonpoliovirus enteroviruses." J Clin Microbiol 31(2): 395-9.
	This report describes a rapid method of detection of poliovirus from viral isolates of clinical specimens using a single set of primers selected from the conserved 5' noncoding region of the poliovirus genome. Of the 144 clinical viral isolates examined, 81 were positive for polioviruses and 50 were positive for nonpoliovirus enteroviruses by tissue culture neutralization and infectivity. All 81 (100%) of the viral isolates identified as poliovirus by tissue culture infectivity were also positive by polymerase chain reaction. Of 50 nonpoliovirus enterovirus isolates found to be negative for poliovirus by tissue culture neutralization and infectivity, 48 were also negative by polymerase chain reaction. The high sensitivity (100%) and specificity (96%) of the primer set indicate that this assay has potential clinical applicability in the diagnosis of nonpoliovirus enterovirus infection.

Abu Al-Soud, W. and P. Radstrom (1998). "Capacity of nine thermostable DNA polymerases To mediate DNA amplification in the presence of PCR-inhibiting samples." Appl Environ Microbiol 64(10): 3748-53.
	The PCR is an extremely powerful method for detecting microorganisms. However, its full potential as a rapid detection method is limited by the inhibition of the thermostable DNA polymerase from Thermus aquaticus by many components found in complex biological samples. In this study, we have compared the effects of known PCR-inhibiting samples on nine thermostable DNA polymerases. Samples of blood, cheese, feces, and meat, as well as various ions, were added to PCR mixtures containing various thermostable DNA polymerases. The nucleic acid amplification capacity of the nine polymerases, under buffer conditions recommended by the manufacturers, was evaluated by using a PCR-based detection method for Listeria monocytogenes in the presence of purified template DNA and different concentrations of PCR inhibitors. The AmpliTaq Gold and the Taq DNA polymerases from Thermus aquaticus were totally inhibited in the presence of 0.004% (vol/vol) blood in the PCR mixture, while the HotTub, Pwo, rTth, and Tfl DNA polymerases were able to amplify DNA in the presence of 20% (vol/vol) blood without reduced amplification sensitivity. The DNA polymerase from Thermotoga maritima (Ultma) was found to be the most susceptible to PCR inhibitors present in cheese, feces, and meat samples. When the inhibitory effect of K and Na ions was tested on the nine polymerases, HotTub from Thermus flavus and rTth from Thermus thermophilus were the most resistant. Thus, the PCR-inhibiting effect of various components in biological samples can, to some extent, be eliminated by the use of the appropriate thermostable DNA polymerase.

Adhin, M. R., J. Alblas, et al. (1990). "Secondary structure at the 3' terminal region of RNA coliphages: comparison with tRNA." Biochim Biophys Acta 1050(1-3): 110-8.
	Secondary structure models for the 3' non-coding region of the four groups of coliphage RNA are proposed based on comparative sequence analysis and on previously published data on the sensitivity of nucleotides in MS2 RNA to chemical modification and enzymes. We report the following observations. (1) In contrast to the coding regions, the structure at the 3' terminus is characterized by stable regular helices. We note the occurrence of the loop sequences 5'-GUUCGC and 5'-CGAAAG, that are reported to confer exceptional stability to stem structures. These features are probably present to promote the segregation of mother and daughter strands during replication. (2) Comparison of homologous helices indicates that only those base pair substitutions are allowed that maintain the thermodynamic stability. (3) We have compared the structure of phage RNA with tRNA. Overall similarity is low, but one common element may exist. It is a quasi-continuous helix of 12 basepairs that could be the equivalent of the 12 basepair long coaxially stacked helix, formed by the T psi C arm and the aminoacyl acceptor arm in tRNA. As in tRNA, this structure element starts after the fourth nucleotide from the 3' end. (4) Phage RNA contains a large variable region of about 35 nucleotides bulging out from the quasi-continuous helix. We speculate that the variable loop in present-day tRNA could be the remnant of the variable region found in phage RNA. The variable region contains overlapping binding sites for the replicase enzyme and the maturation protein. This common binding site may serve as a switch from replication to packaging.

Adhin, M. R., A. Avots, et al. (1990). "Complete nucleotide sequence of the group I RNA bacteriophage fr." Biochim Biophys Acta 1050(1-3): 104-9.
	We report the complete nucleotide sequence of the group I RNA bacteriophage fr. The entire genome consists of 3575 nucleotides, six nucleotides more than the only other sequenced group I representative, MS2. The greatest divergence between these phages occurs in the 5' terminal region of the A gene, while the lysis-replicase gene overlap, the coat gene and the central region of the replicase gene are highly conserved. Overall sequence homology between fr and MS2 is 77%. Here, we present a general comparison between the two phages. In the accompanying paper we use phylogenetic sequence comparison between MS2 and fr to deduce the secondary structure at the 3' untranslated region.

Afzal, M. A. and P. D. Minor (1994). "Instant RNA isolation from virus-infected tissue culture fluid for the polymerase chain reaction." Vaccine 12(11): 976-7.
	This paper describes an efficient method of RNA isolation, enabling RNA templates to be obtained for reverse transcription within 20 min. The procedure avoids the use of hazardous organic chemicals and ethanol precipitation, and does not require ultracentrifugation. Results are presented for extraction of RNA from virus-infected tissue culture fluid, infected cell sheets, vaccine bulk material and lyophilized commercial vaccines.

Aggarwal, R., S. Kamili, et al. (2001). "Experimental studies on subclinical hepatitis E virus infection in cynomolgus macaques." J Infect Dis 184(11): 1380-5.
	Serial subclinical transmission among susceptible humans may serve as a reservoir of hepatitis E virus (HEV) in areas in which HEV is endemic. This hypothesis was investigated in an experimental primate model. Four groups of 4 cynomolgus macaques each were inoculated intravenously with 10(4)-10(5) (group 1), 10-100 (group 2), and 1-10 (group 3) cynomolgus macaque HEV infectious doses. All 4 animals in group 1 had clinical disease marked by alanine aminotransferase (ALT) elevation, fecal virus excretion, viremia, and seroconversion. Of the animals in groups 2 and 3, only 1 had evidence of biochemical hepatitis, although most had virus excretion and viremia (3 animals each in groups 2 and 3), and evidence of seroconversion (1 animal in group 2 and 3 animals in group 3). Viral genomic titers in stool specimens of animals with or without ALT elevation were similar. Infectivity studies confirmed the viability and transmission potential of the virus excreted by animals without ALT elevation. These data suggest that subclinical HEV infection may represent an HEV reservoir.

Aggarwal, R. and K. A. McCaustland (1998). "Hepatitis E virus RNA detection in serum and feces specimens with the use of microspin columns." J Virol Methods 74(2): 209-13.
	This report describes the use of microspin columns for extraction of hepatitis E virus (HEV) RNA from stool and serum specimens for reverse transcription-polymerase chain reaction (RT-PCR) and compares this method with the glass powder method. The microspin column method was found to be 1- to 2-log more sensitive in detecting HEV RNA than the glass powder method and had better reproducibility. The microspin column method also detected HEV RNA in a larger number of specimens than the glass powder method from among a panel of serum and stool specimens. Use of this method may allow better assessment of viremia and fecal excretion in patients and experimental animals infected with HEV.

Aggarwal, R. and S. Naik (2008). Enterically transmitted hepatitis. Food-Borne Viruses: Progress and Challenges. M. P. G. Koopmans, D. O. Cliver, and A. Bosch Washington, DC, ASM (American Society for Microbiology) Press: 65-85.
	
Aggarwal, R. and S. R. Naik (1992). "Faecal excretion of hepatitis E virus." Lancet 340(8822): 787.
	
Aggarwal, R. and S. R. Naik (1994). "Hepatitis E: intrafamilial transmission versus waterborne spread." J. Hepatol. 21(5): 718-723.
	The relative significance of intrafamilial transmission and continued water contamination in the spread of hepatitis E is not known. To resolve this question, two surveys were conducted during a large bimodal waterborne epidemic of hepatitis E in Kanpur, India, affecting an estimated 79,000 persons: i) April 1991: covering 420 houses (60 houses each in seven municipal wards) selected using multistage sampling and random number tables, and ii) May 1992: covering the same families in five municipal wards with incidence rates exceeding 1.5% in the first survey. The number of affected cases in each family and the time of onset of disease in each case were recorded. The time interval between the first ('index') case and the subsequent ('later') case(s) in each family was calculated. The temporal relationship of the occurrence of cases was correlated with the time of control of water contamination. One hundred and eleven hepatitis cases occurred in the 343 families (with 2018 members) studied. Eighty-one of these were single or first cases in their families. Twenty-two 'later' cases occurred within 2 weeks (minimum incubation period of hepatitis E) of the 'index' cases and could not be due to intrafamilial transmission. Thus, 103 of 111 (92.8%) cases were due to primary waterborne infection. Eight 'later' cases (7.2% of 111) that occurred 2-6 weeks after the index cases could be due either to direct spread or to intrafamilial transmission. No 'later' case occurred more than 6 weeks after the 'index' cases. New cases stopped appearing 9 weeks (upper limit of incubation period of hepatitis E) after steps to check water contamination were taken.(ABSTRACT TRUNCATED AT 250 WORDS)

Aggarwal, R. and S. R. Naik (1997). "Epidemiology of hepatitis E: past, present and future." Trop Gastroenterol 18(2): 49-56.
	
Aggarwal, R., H. Shahi, et al. (1997). "Evidence in favour of high infection rate with hepatitis E virus among young children in India." J Hepatol 26(6): 1425-6.
	
Agnès, F., J. M. Crance, et al. (1994). "Separate detection of the two complementary RNA strands of hepatitis A virus." Journal of Virological Methods 49(3): 323-330.
	The minus strand of hepatitis A virus can be detected specifically by reverse transcription and polymerase chain reaction amplification in infected cell culture extracts. Several controls gave evidence that the amplified fragment actually used the minus strand as initial template. Non-thermostable reverse transcriptase was not efficient for this purpose because of self-priming of the positive-stranded viral RNA during the reverse transcription step. This problem was overcome by the use of the thermostable rTth DNA polymerase that also has reverse transcriptase activity in the presence of Mn2+. 

Agol, V. I., G. A. Belov, et al. (2000). "Competing death programs in poliovirus-infected cells: commitment switch in the middle of the infectious cycle." J Virol 74(12): 5534-41.
	Productive poliovirus infection of HeLa cells leads to the canonical cytopathic effect (CPE), whereas certain types of abortive infection result in apoptosis. To define the time course of commitment to the different types of poliovirus-induced death, inhibitors of viral replication (guanidine HCl) or translation (cycloheximide) were added at different times postinfection (p.i.). Early in the infection (during the first approximately 2 h p.i.), predominantly proapoptotic viral function was expressed, rendering the cells committed to apoptosis, which developed several hours after viral expression was arrested. In the middle of infection, concomitantly with the onset of fast generation of viral progeny, the implementation of the viral apoptotic program was abruptly interrupted. In particular, activation of an Asp-Glu-Val-Asp (DEVD)-specific caspase(s) occurring in the apoptosis-committed cells was prevented by the ongoing productive infection. Simultaneously, the cells retaining normal or nearly normal morphology became committed to CPE, which eventually developed regardless of whether or not further viral expression was allowed to proceed. The implementation of the poliovirus-induced apoptotic program was suppressed in HeLa cells overexpressing the Bcl-2 protein, indicating that the fate of poliovirus-infected cells depends on the balance of host and viral pro- and antiapoptotic factors.

Aguzzi, A., T. Blattler, et al. (1997). "Tracking prions: the neurografting approach." Cell Mol Life Sci 53(6): 485-95.
	The physical nature of the agent that causes transmissible spongiform encephalopathies (the 'prion'), is the subject of passionate controversy. Investigation of it has benefited tremendously from the use of transgenic and knockout technologies. However, prion diseases present several other enigmas, including the mechanism of brain damage and how the affinity of the agent for the central nervous system is controlled. Here we show that such questions can be effectively addressed in transgenic and knockout systems, and that pathogenesis may be clarified even before we can be certain about the nature of the infectious agent. Availability of mice overexpressing the Prnp gene (which encodes the normal prion protein) and Prnp knockout mice allows for selective reconstitution experiments aimed at expressing PrP in specific portions of the brain or in selected populations of hemato- and lymphopoietic origin. We summarize how such studies can offer insights into how prions administered to peripheral sites can gain access to central nervous tissue, and into the molecular requirements for spongiform brain damage.

Aguzzi, A., A. Raeber, et al. (1997). "Neurotoxicity and neuroinvasiveness of prions." J Neurovirol 3 Suppl 1: S23-4.
	
Airaksinen, A., M. Roivainen, et al. (1999). "Site-saturation mutagenesis of the PALTAVETG motif in coxsackievirus A9 capsid protein VP1 reveals evidence of conservation of a periodic hydrophobicity profile." J Gen Virol 80 ( Pt 8): 1919-27.
	Enteroviruses possess a highly conserved 9 amino acid stretch of mainly hydrophobic character in the capsid protein VP1. A novel strategy, combining site-saturation mutagenesis and a single-tube cloning and transfection procedure, has been developed for the analysis of this motif in coxsackievirus A9 (CAV-9). Four individual amino acids were separately mutated. Mutagenesis of three of the four positions in CAV-9 resulted in a number of viable but impaired mutant strains, each containing a single amino acid substitution. In contrast, no mutants with amino acid substitutions at leucine 31 were isolated, although three different leucine codons were found among the viruses recovered. Small plaque size was regularly associated with reduced yields of infectious virus and an amino acid substitution at the target site in the viruses isolated from the site-saturated virus pools. From the range of amino acids observed in viable mutants, it was possible to estimate the characteristics that are required at individual amino acid positions. It seems that in the motif studied here, a periodic hydrophobicity profile needs to be conserved. The constraints observed on the ranges of acceptable amino acids presumably reflect the structural-functional requirements that have resulted in the conservation of the motif.

Aldabe, R., A. Barco, et al. (1996). "Membrane permeabilization by poliovirus proteins 2B and 2BC." Journal of Biological Chemistry 271(38): 23134-7.
	Poliovirus infection leads to drastic alterations in membrane permeability late during infection. Transient expression of each nonstructural protein of poliovirus by means of recombinant vaccinia virus encoding the T7 RNA polymerase indicates that proteins 2B and 2BC strongly enhance membrane permeability to hygromycin B in HeLa cells. Almost no effect on expression of proteins 2C, 3A, 3AB, and 3C was found. Deletions and point mutations in 2B and 2BC have identified sequences in 2B involved in membrane permeabilization. Regions located at both ends of 2B are necessary to bring about these permeability alterations. A deletion of 11 amino acids of 2BC at the junction between 2B and 2C, as well as long deletions in 2C encompassing the GTPase motifs of this protein, do not impair the capacity of 2BC to modify the permeability of the membrane. The release of compounds such as choline or uridine from preloaded cells is also augmented by 2B and 2BC expression.

Alexandersen, S., M. Quan, et al. (2003). "Studies of quantitative parameters of virus excretion and transmission in pigs and cattle experimentally infected with foot-and-mouth disease virus." J Comp Pathol 129(4): 268-82.
	Foot-and-mouth disease virus (FMDV) can be spread by a variety of mechanisms and the rate of spread, the incubation period and the severity of disease depend on a multitude of parameters, including the strain of virus, the dose received, the route of introduction, the animal species and the husbandry conditions. More knowledge with regard to these parameters is urgently needed to improve resource-efficient disease control. This report describes detailed studies of FMDV load, excretion and transmission in pigs infected with FMDV O UKG 2001, O TAW 1997 and C Noville virus and in cattle infected with the O UKG 2001 virus to facilitate use of a "FMDV load framework" for the assessment of transmission risks. Virus replicated rapidly in pigs and cattle exposed by direct contact. The mean incubation period was around 3-4 days for cattle-to-cattle and 1-3 days for pig-to-pig transmission, depending on the intensity of contact. The results confirmed that a strong relation exists between dose and length of incubation period. Clinical disease was severe in pigs but relatively mild in inoculated cattle; contact infection of cattle appeared to increase the severity of lesions. FMDV RNA was recovered in nasal and mouth swabs from inoculated animals soon after they developed a viraemia and probably reflected the early production and excretion of virus. FMDV RNA in nasal and mouth swabs from contact animals could be detected several days before they showed other signs of infection, indicating the possibility of detecting exposed animals during the incubation period. FMDV RNA could also be detected in swab samples after the viraemic phase. This may have represented background environmental virus that had been trapped in the respiratory tract and mouth. Alternatively, it may have indicated a somewhat slower clearance or half-life of viral RNA or an extended low level of FMDV replication at these sites. The pattern of FMDV RNA concentrations in pigs was closely similar to that in cattle, but the amounts of FMDV RNA were higher.

Alexandersen, S., Z. Zhang, et al. (2003). "The pathogenesis and diagnosis of foot-and-mouth disease." J Comp Pathol 129(1): 1-36.
	The pathogenesis of foot-and-mouth disease (FMD) is reviewed, taking account of knowledge gained from field and experimental studies and embracing investigations at the level of the virus, the cell, the organ, the whole animal and the herd or flock. The review also addresses the immune response and the carrier state in FMD. Progress made in understanding the pathogenesis of the disease is highlighted in relation to developments in diagnosis and methods of control.

Alhajjar, B. J., S. L. Stramer, et al. (1988). "Transport modelling of biological tracers from septic systems." Water Research 22: 907-915.
	
Ali, M. A., A. Z. Al-Herrawy, et al. (2004). "Detection of enteric viruses, Giardia and Cryptosporidium in two different types of drinking water treatment facilities." Water Res 38(18): 3931-9.
	In this study, two types of drinking water treatment facilities (two conventional drinking water treatment plants (DWTPs) and two compact units (Cus)) were compared referring to their production capacity. Water samples were collected from three main points: (a) different water treatment steps (b) washings of sand filters and (c) distribution system at different distances from the water treatment plants. Both viruses and protozoa were concentrated from each water sample by adsorption and accumulation on the same nitrocellulose membrane filters (0.45 microm pore size). Enteroviruses were detected by plaque infectivity assay in BGM cells and HAV, HEV and Norovirus were detected by RT-PCR. Giardia and Cryptosporidium were detected by conventional staining methods and PCR. The results revealed that enterovirus load at the intake ranged between 10-15 PFU/L for the two compact units and between 4.5 and 75 PFU/L for the two conventional DWTPs. The virus load in distribution system of the first type DWTPs at 1 km from the plant was the same as that of the intake. Viruses in the other type of treatment plants CUs at 1, 5 and 7 km, were much reduced. Investigation of raw water sediments of the two DWTPs showed enterovirus counts between 12 and 17.5 PFU/L. Virus count was reduced in sand of filters after washing. Giardia cysts were equally detected by microscopy and PCR in only intake samples of EL-Hawamdia CU (33.3%) and Meet Fares DWTP (50%). Cryptosporidium oocysts were equally detected by microscopy and PCR in intake samples of Abo EL-Nomros CU (100%), EL-Hawamdia CU (66.7%) and Fowa DWTP (50%). At Meet Fares DWTP three positive intake samples for Cryptosporidium were detected by PCR, compared with only two positive samples by microscopy. Giardia cysts and Cryptosporidium oocysts were detected in raw water sediment and sand of filters before washing. Only one sample from Meet Fares DWTP sand of filters after washing was positive for both Giardia and Cryptosporidium. It can be concluded that the poor microbial quality of the water may be due to improper operational skills and management of the various water treatment plants (especially at the two high capacity treatment plants).

Allard, A., B. Albinsson, et al. (1992). "Detection of adenoviruses in stools from healthy persons and patients with diarrhea by two-step polymerase chain reaction." J Med Virol 37(2): 149-57.
	The use of the polymerase chain reaction (PCR) for detection of human adenoviruses in diluted stool samples was investigated. Two sets of nested primers, including primers specific for the hexon-coding region and for the E1B region of enteric adenoviruses (EAd), were assessed by two-step amplification. The primers constitute two different PCR systems designed for the detection of adenoviruses belonging to all six subgenera (A-F), and the two EAds Ad40 and Ad41, respectively. In a two-step PCR mediated amplification a single virus particle was detected when the two sets of general hexon primers or EAd specific primers were used. Earlier results from PCR detection of adenoviruses in stool from children suffering from diarrhea gave indications that adenovirus particles are commonly shed in stools without being identified as the cause of illness [Allard et al.: Journal of Clinical Microbiology 28:2659-2667, 1990]. Therefore, the general and the EAd specific PCR assays were assessed on 150 stool specimens from three groups including 50 healthy children, 50 healthy adults, and 50 adults suffering from diarrhea. When the two sets of general hexon primers were used, 25 of the 50 specimens from the healthy children (mean age 21 months) were found positive by two-step PCR amplification. Nine of the 50 specimens from the healthy adults (mean age 32 years) were found positive whereas 12 of the 50 specimens from sick adults (mean age 31 years) gave amplification products, using the two sets of general hexon primers in a nested fashion. None of the 150 specimens were found to be positive by two-step PCR amplification using the two sets of EAd-specific primers.(ABSTRACT TRUNCATED AT 250 WORDS)

Allard, A., B. Albinsson, et al. (2001). "Rapid typing of human adenoviruses by a general PCR combined with restriction endonuclease analysis." J Clin Microbiol 39(2): 498-505.
	We have developed a system for rapid typing of adenoviruses (Ads) based on a combination of PCR and restriction endonuclease (RE) digestion (PCR-RE digestion). Degenerated consensus primers were designed, allowing amplification of DNA from all 51 human Ad prototype strains and altogether 44 different genome variants of Ad serotypes 1, 3, 4, 5, 7, 11, 19, 40, and 41. The 301-bp amplimer of 22 prototype strains representing all six subgenera and the genome variant was selected as a target for sequencing to look for subgenus and genome type variabilities. The sequences obtained were used to facilitate the selection of specific REs for discrimination purposes in a diagnostic assay by following the concept of cleavage or noncleavage of the 301-bp amplimer. On the basis of these results, a flowchart was constructed, allowing identification of subgenus B:2 and D serotypes and almost complete distinction of subgenus A, B:1, C, E, and F serotypes. Application of the PCR-RE digestion system to clinical samples allowed typing of 34 of 40 clinical samples positive for Ad. The genome type determined by this method was identical to that obtained by traditional RE typing of full-length Ad DNA. The remaining six samples were positive only after a nested PCR. Therefore, to reduce the risk of false-negative results, samples scored negative by the PCR-RE digestion system should be evaluated by the described nested PCR. Used in combination, the PCR-RE digestion method and the nested PCR provide a reliable and sensitive system that can easily be applied to all kinds of clinical samples when rapid identification of adenoviruses is needed.

Allard, A., P. J. R. Girones, et al. (1990). "Polymerase chain reaction for detection of adenoviruses in stool samples." Journal of Clinical Microbiology 28(12): 2659-2667.
	The usefulness of the polymerase chain reaction (PCR) method for diagnosing adenovirus infections was investigated. Several primers, including primers specific for the hexon-coding region and for enteric adenovirus types 40 and 41, were evaluated. The PCR method was validated against cell culturing in routine diagnostic work and against restriction enzyme analysis of viral DNA. Sixty diagnostic specimens were selected for evaluation by the PCR method. Twenty of the 60 specimens were found positive on the basis of cytopathic effects and latex agglutination (Adenolex [Orion Diagnostica, Helsinki, Finland]), and 16 were identified and typed as adenoviruses by polyacrylamide gel electrophoresis. PCR was performed on all 60 specimens in parallel directly on diluted stool samples and on viral DNA extracted from cells inoculated with the same stool samples. When the general hexon primers were used 51 of the 60 specimens from infected cell cultures were found positive by PCR, whereas only 13 specimens were found positive when PCR was performed directly on stool samples. With the use of selective primers for enteric adenoviruses 16 of the 60 cell cultures were found to exhibit amplification products by PCR, whereas 4 were detected in stool samples. None of the 60 specimens were found positive by PCR when an adenovirus type 40-specific primer pair was used. PCR was found to be a fast, sensitive, and reliable method for the detection of adenoviruses in diarrheal disease, provided the amplifications were performed directly on diluted stool samples. 

Allwood, P. B., Y. S. Malik, et al. (2003). "Survival of F-specific RNA coliphage, feline calicivirus, and Escherichia coli in water: a comparative study." Appl Environ Microbiol 69(9): 5707-10.
	The relationship between the survival of enteric viral pathogens and their indicators (coliform bacteria and coliphages) is not well understood. We compared the survival rates of feline calicivirus (FCV), Escherichia coli, and a male-specific RNA coliphage MS2 at 4, 25, and 37 degrees C for up to 28 days in dechlorinated water. The survival rates of E. coli and FCV, a surrogate of noroviruses (NV), had a high degree of correlation at 4 and 25 degrees C, while MS2 phage survived significantly longer (P < 0.05) at these two temperatures. At 37 degrees C, the survival rates for all three organisms were highly correlated. Decimal reduction values indicating the number of days needed for 90% reduction in titer (D values) decreased for all three organisms as storage temperatures increased. FCV had the shortest D value among all three organisms at all temperatures investigated. These findings indicate that F-specific RNA phages may be useful indicators of NV in the environment.

Allwood, P. B., Y. S. Malik, et al. (2004). "Effect of temperature and sanitizers on the survival of feline calicivirus, Escherichia coli, and F-specific coliphage MS2 on leafy salad vegetables." J Food Prot 67(7): 1451-6.
	We conducted a series of experiments to compare the survival of Escherichia coli, feline calicivirus, and F-specific coliphage MS2 on lettuce and cabbage with and without disinfection. Inoculated produce was held at 4, 25, or 37 degrees C for 21 days or was treated with different concentrations of sodium bicarbonate, chlorine bleach, peroxyacetic acid, or hydrogen peroxide. Survival was measured by the decimal reduction value (time to 90% reduction in titer) and the change in log titers of the test organisms. A stronger correlation of survival measures was observed between feline calicivirus and MS2 than between E. coli and either of the viral agents at 25 and 37 degrees C. The maximum time to detection limit for MS2 at all temperatures was 9 days, whereas feline calicivirus was detected for a maximum of 14 days at 4 degrees C. In contrast, E. coli was detectable for 21 days at 4 and 25 degrees C and for 14 days at 37 degrees C. Significant increases in E. coli titer occurred within the first 5 days, but virus titers decreased steadily throughout the experiments. E. coli was also highly susceptible to all disinfectants except 1% sodium bicarbonate and 50 ppm chlorine bleach, whereas the viruses were resistant to all four disinfectants.

Allwood, P. B., Y. S. Malik, et al. (2005). "Effect of Temperature on the Survival of F-Specific RNA Coliphage, Feline Calicivirus, and Escherichia coli in Chlorinated Water." Int J Environ Res Public Health 2(3-4): 442-6.
	We compared the survival of F-specific RNA coliphage MS2, feline calicivirus, and E. coli in normal tap water and in tap water treated to an initial concentration of 50 ppm free chlorine and held at 4 degrees C, 25 degrees C, or 37 degrees C for up to 28 days. Our aim was to determine which of these two organisms (coliphage or E. coli) was better at indicating norovirus survival under the conditions of the experiment. There was a relatively rapid decline of FCV and E. coli in 50 ppm chlorine treated water and both organisms were undetectable within one day irrespective of the temperature. In contrast, FRNA phage survived for 7 to 14 days in 50 ppm chlorine treated water at all temperatures. All organisms survived for 28 days in tap water at 4 degrees C, but FCV was undetectable on day 21 and day 7 at 25 degrees C and 37 degrees C, respectively. Greater survival of FRNA phage compared to E. coli in 50 ppm chlorine treated water suggests that these organisms should be further investigated as indicators of norovirus in depurated shellfish, sanitized produce, and treated wastewater which are all subject to high-level chlorine treatment.

Allwood, P. B., Y. S. Malik, et al. (2004). "Occurrence of Escherichia coli, noroviruses, and F-specific coliphages in fresh market-ready produce." J Food Prot 67(11): 2387-90.
	Forty samples of fresh produce collected from retail food establishments were examined to determine the occurrence of Escherichia coli, F-specific coliphages, and noroviruses. An additional six samples were collected from a restaurant undergoing investigation for a norovirus outbreak. Nineteen (48%) of the retail samples and all outbreak samples were preprocessed (cut, shredded, chopped, or peeled) at or before the point of purchase. Reverse transcription-PCR, with the use of primers JV 12 and JV 13, failed to detect norovirus RNA in any of the samples. All six outbreak samples and 13 (33%) retail samples were positive for F-specific coliphages (odds ratio undefined, P = 0.003). Processed retail samples appeared more likely to contain F-specific coliphages than unprocessed samples (odds ratio 3.8; 95% confidence interval 0.8 to 20.0). Only two (5.0%) retail samples were positive for E. coli; outbreak samples were not tested for E. coli. The results of this preliminary survey suggest that F-specific coliphages could be useful conservative indicators of fecal contamination of produce and its associated virological risks. Large-scale surveys should be conducted to confirm these findings.

Alouini, S. and M. D. Sobsey (1995). "Evaluation of an extraction-precipitation method for recovering hepatitis A virus and poliovirus from hardshell clams (Mercenaria mercenaria)." Water Science and Technology 31(5-6): 465-469.
	
Alter, M. J. (1982). "Unpublished information." Centers for Disease Control, Phoneix, AZ.
	
Alter, M. J., R. J. Gerety, et al. (1982). "Sporadic non-A, non-B hepatitis: frequency and epidemiology in an urban U.S. population." Journal of Infectious Diseases 145(6): 886-893.
	Patients with acute viral hepatitis were identified at five hospitals in Baltimore, Maryland between February 1979-August 1980. Of the 295 patients with serologically diagnosed hepatitis, 42% had non-A, non-B hepatitis; 48% had hepatitis B; and 10% had hepatitis A. Compared with matched control patients with no liver disease, patients with non-A, non-B hepatitis more often had received a blood transfusion (11% vs. O, P less than 0.001), used parenteral drugs (42% vs. 4%, P less than 0.001), were employed as health workers in direct patient care or hospital laboratory work (6% vs. 3%, P less than 0.05), had personal contact with others who had hepatitis (16% vs. 1%, P less than 0.001), or had ingested raw shellfish (34% vs. 20%, P less than 0.01). A history of previous clinical hepatitis and serologic markers indicating previous hepatitis B infection were found in patients with non-A, non-B hepatitis more often than in the control patients. Chronic non-A, non-B hepatitis was found in 34 (42.5%) of 80 patients with non-A, non-B hepatitis. 

Altschul, S. F., T. L. Madden, et al. (1997). "Gapped BLAST and PSI-BLAST: a new generation of protein database search programs." Nucleic Acids Res 25(17): 3389-402.
	The BLAST programs are widely used tools for searching protein and DNA databases for sequence similarities. For protein comparisons, a variety of definitional, algorithmic and statistical refinements described here permits the execution time of the BLAST programs to be decreased substantially while enhancing their sensitivity to weak similarities. A new criterion for triggering the extension of word hits, combined with a new heuristic for generating gapped alignments, yields a gapped BLAST program that runs at approximately three times the speed of the original. In addition, a method is introduced for automatically combining statistically significant alignments produced by BLAST into a position-specific score matrix, and searching the database using this matrix. The resulting Position-Specific Iterated BLAST (PSI-BLAST) program runs at approximately the same speed per iteration as gapped BLAST, but in many cases is much more sensitive to weak but biologically relevant sequence similarities. PSI-BLAST is used to uncover several new and interesting members of the BRCT superfamily.

Alvarez, M. E., M. Aguilar, et al. (2000). "Inactivation of MS-2 phage and poliovirus in groundwater." Can J Microbiol 46(2): 159-65.
	Since temperature affects the inactivation rate of viruses in natural water systems, the aim of this study was to determine if a temperature shift could influence the structural integrity of model viruses. When crude lysates of MS-2 phage were seeded into groundwater microcosms and incubated at 27 degrees C, complete virus inactivation took place in eight days. The temperature was then shifted to 4 degrees C. Three days after the temperature shift, a two-log increase in virus titer (reactivation) occurred. However, when purified MS-2 lysates were added to groundwater microcosms, no reactivation was obtained. No reactivation of poliovirus took place when similar microcosm experiments were done. The sedimentation coefficients of MS-2 shifted from 80S to 58S, 48S, 37S, 32S, and 18S as inactivation proceeded in groundwater and distilled water controls. Similarly, the sedimentation coefficients of polioviruses changed from 156S to 142S, 135S, 117S, 105S, 95S, and 80 S as inactivation took place. There was no correlation between % virus inactivation and % decrease in virions with intact sedimentation coefficients, as reported earlier for poliovirus inactivated by chlorine. The results presented support our hypothesis that virus inactivation proceeds gradually, involving the rearrangement and (or) loss of capsomere components that may eventually lead to the ejection of nucleic acids. The intermediate particles generated as inactivation proceeds may be in a reversibly inactivated state, and may revert back to a fully infectious state when chemical components stabilize the virus particle.

Alvarez, M. E. and R. T. O'Brien (1982). "Effects of chlorine concentration on the structure of poliovirus." Applied and Environmental Microbiology 43(1): 237-239.
	Chlorine concerntrations below 0.8 mg/liter inactivated poliovirus without causing separation of the viral of the viral components. These results indicate that the release of RNA from the capsids is the result, not the cause, of virus inactivation by chlorine.

Alvarez, M. E. and R. T. O'Brien (1982). "Mechanisms of inactivation of poliovirus by chlorine dioxide and iodine." Applied and Environmental Microbiology 44(5): 1064-71.
	Chlorine dioxide and iodine inactivated poliovirus more efficiently at pH 10.0 than at pH 6.0. Sedimentation analyses of viruses inactivated by chlorine dioxide and iodine at pH 10.9 showed that viral RNA separated from the capsids, resulting in the conversion of virions from 156S structures to 80S particles. The RNAs release from both chlorine dioxide- and iodine-inactivated viruses cosedimented with intact 35S viral RNA. Both chlorine dioxide and iodine reacted with the capsid proteins of poliovirus and changed the pI from pH 7.0 to pH 5.8. However, the mechanisms of inactivation of poliovirus by chlorine dioxide and iodine were found to differ. Iodine inactivated viruses by impairing their ability to adsorb to HeLa cells, whereas chlorine dioxide-inactivated viruses showed a reduced incorporation of [14C]uridine into new viral RNA. We concluded, then, that chlorine dioxide inactivated poliovirus by reacting with the viral RNA and impairing the ability of the viral genome to act as a template for RNA synthesis.

Alvarez-Munoz, M. T., J. Torres, et al. (1999). "Seroepidemiology of hepatitis E virus infection in Mexican subjects 1 to 29 years of age." Arch Med Res 30(3): 251-4.
	BACKGROUND: Hepatitis E virus (HEV) infection causes an acute, self-limited hepatitis associated with high mortality in pregnant women. Community-based surveys are scarce and information on HEV infection in populations is needed. The aim of this work was to study seroprevalence to HEV in young adults and children in Mexico, using a community-based survey. METHODS: Serum samples from 3,549 individuals were studied; the population included subjects from 1 to 29 years old from all regions of the country representing all socioeconomic levels. IgG anti-HEV was determined by ELISA. RESULTS: Anti-HEV antibodies were found in 374 (10.5%) individuals. Seroprevalence increased with age from 1.1% in children younger than 5 years to 14.2% in persons 26 to 29 years of age (p = 0.006). Risk factors for infection included living in rural communities and a low educational level. Seroprevalence was not associated with the level of regional development. CONCLUSIONS: HEV infection is endemic in Mexico. Age, type of community, and educational level were identified as risk factors for infection.

Amahmid, O., S. Asmama, et al. (1999). "The effect of waste water reuse in irrigation on the contamination level of food crops by Giardia cysts and Ascaris eggs." International Journal of Food Microbiology 49(1-2): 19-26.
	In Marrakech, raw sewage has been used for farming purposes for several decades for many types of crops. This study aimed to determine the contamination level of Giardia cysts and Ascaris eggs for crops designated for human consumption. Collected crops in irrigated fields were turnip, marrow, squash, potatoes, pepper and eggplant. Field trials were also carried out on four crops, coriander, carrots, mint and radish, using three water types for irrigation, i.e. raw waste water, treated waste water (sedimentation and 16 days retention) and fresh water. Giardia cysts were detected at a level of 5.1 cysts/kg in potatoes, while Ascaris eggs were observed in numbers varying between 0.18 eggs/kg in potatoes and 0.27 eggs/kg in turnip. Field trials confirmed that irrigation of crops by raw waste water leads to contamination. Giardia and Ascaris were isolated in coriander at concentrations of 254 cysts/kg and 2.7 eggs/kg, respectively; mint was also highly contaminated with numbers reaching 96 cysts/kg and 4.63 eggs/kg. Carrots and radish were contaminated and respective numbers observed for Giardia were 155 and 59.1 cysts/kg; Ascaris was discovered in numbers of 0.7 and 1.64 eggs/kg, respectively. However, cultures irrigated with treated waste water and fresh water were free from contamination. Cysts and eggs on coriander persisted for a maximum of 8 days. 

Ambert-Balay, K., F. Bon, et al. (2005). "Characterization of new recombinant noroviruses." J Clin Microbiol 43(10): 5179-86.
	Noroviruses are important etiologic agents of acute gastroenteritis and show great genetic diversity. To characterize more fully previously detected strains that could not be assigned unequivocally to one particular genotype based on the RNA polymerase, we have sequenced a region in the capsid gene and, in some cases, in the junction between open reading frame 1 (ORF 1) and ORF 2. The results allowed us to identify several recombinant noroviruses: GGIIb viruses were detected for the first time in France in August 2000 and then spread through France and to Europe during the following winter. Here we present the characterization of three other probable GII recombinants which showed different phylogenetic positions depending on their ORF 1 and ORF 2 sequences. Analysis of the region located between ORF 1 and ORF 2 by a nucleotide identity window search showed a sudden shift in similarities. Moreover, recombination breakpoints were identified upstream and downstream of the beginning of ORF 2 by using a statistical test, thus confirming the involvement of this region in recombination. Unlike GGIIb, the three recombinants described here do not seem to have diffused widely in the community: one was found in a waterborne outbreak, and the other two were found in sporadic cases. Recombination is important for the evolution of RNA viruses and has already been described for noroviruses. Our results suggest that recombination is not a rare phenomenon among noroviruses, but not all these presumed recombinants that formed during RNA replication are able to spread widely.

Ambros, V. and D. Baltimore (1980). "Purification and properties of a HeLa cell enzyme able to remove the 5'- terminal protein from poliovirus RNA." Journal of Biological Chemistry 255(14): 6739-44.
	Using a rapid phenol extraction assay, an enzyme was purified from uninfected HeLa cells that can cleave the 5'-terminal protein (VPg) from poliovirus RNA. Both cytoplasmic and nuclear extracts had enzymes with similar behavior. A polypeptide of molecular weight 27,000 was the major one present in the purified preparation. Assuming that this protein is the enzyme, a very low turnover number was calculated for it. The purified enzyme would cleave the tyrosine-phosphate bond linking VPg to poliovirus RNA with minimal degradation of the RNA or of VPg. If the RNA was first treated with proteinase K to degrade VPg, leaving a small peptide on the RNA, this peptide could also be removed by the enzyme. If the RNA was degraded with T1 RNase, leaving VPg attached to a nonanucleotide, the enzyme still would cleave off VPg, although incompletely. If the RNA was degraded completely, leaving either pUp or pU attached to VPg, the enzyme would not remove the nucleotides from the protein. Thus, for the enzyme to be active requires some length of polynucleotide attached to the protein but only a short peptide need be present for the enzyme to act.

Amela, C., I. Pachón, et al. (1995). "Trends in hepatitis A virus infection with reference to the process of urbanization in the greater Madrid area (Spain)." European Journal of Epidemiology 11(5): 569-573.
	Hepatitis A is an infection transmitted by the fecal-oral route. Endemicity within a specific country is directly related to sanitation and hygienic standards, while being inversely related to socioeconomic conditions. We studied how the process of urbanization witnessed in Madrid had influenced the transmission of hepatitis A infection. In the Madrid Autonomous Region, this process first began in the early sixties and was not brought to a close until the late seventies. Catalytic models were used to estimate the annual infection rate, lambda, on the basis of seroprevalence data stratified by age. A cohort effect related to a fall-off in infancy-related hepatitis A virus (HAV) is to be observed in the results for the last few years. The model permits four birth cohort-based groups to be differentiated by lambda: individuals born pre-1960, lambda = 0.082 (95% CI 0.095-0.070); those born in the early sixties, lambda = 0.052 (95% CI 0.060-0.042); whose members were born in the late sixties, lambda = 0.033 (95% CI 0.041-0.025); and those born in the late seventies, lambda = 0.017 (95% CI 0.020-0.013). The first group includes those born before the urbanization process had started. The second and third groups coincide with the development stage of that process, hence exhibiting transitional rates. The fourth group reflects the process in its consolidation stage. This reduction in the transmission of infection has changed the manner of presentation, so that while isolated cases or small outbreaks tend to be more common nowadays, occasionally epidemics may evolve explosively. The average age at presentation has risen and the likelihood of symptomatic infection is higher.

Amundson, D., C. Lindholm, et al. (1988). "Microbial pollution of well water in southeastern Minnesota." Journal of Environmental Science and Health A23(5): 453-468.
	Groundwater contamination is a growing problem in southeastern Minnesota. This region is characterized by karst topography which is responsible for the formation of sinkholes, subsurface cracks, and underground rivers. These features enhanced transportation of surface contaminants into groundwater. The present study was conducted to determine the presence of coliforms, fecal coliforms and coliphages in private rural wells situated in this region. Another purpose was to study the oocurrence of drug resistance in bacteria isolated from groundwater. Well water from 18 sites was tested monthly for a period of 16 months . Seventeen of 18 sites sampled showed detectable levels of indicator bacteria. A total of 161 samples were tested for the presence of coliphages. Of these, 13 samples from 7 sites were found positive. On two occasions, coliphages were isolated from samples in which coliforms were undetectable. Water from 10 sites yielded drug resistant indicator bacteria. Twenty-five of 38 (65.8%) total coliforms and 9 of 27 (33.3%) fecal coliforms tested were found to carry drug resistance.

Anders, W. and T. Kima (1959). "On the epidemiology of hepatitis epidemica in Germany." Zentralblatt für Bakteriologie, Parasitenkunde, Infektionskrankheiten und Hygiene I. Original 176: 1-34.
	
Andersen, F. R., F. G. Birkeland, et al. (1996). "[Outbreak of food-borne gastroenteritis caused by a Norwalk-like virus. Evaluation of methods for confirmation of the etiology in suspected viral gastroenteritis]." Tidsskr Nor Laegeforen 116(28): 3325-8.
	Acute gastroenteritis is a common disease and can be food-borne. We describe an outbreak of acute gastroenteritis, probably caused by Norwalk-like virus, which struck 250 people in the course of one week in a small Norwegian community. The source of the infection was probably an infected food handler in a bakery who contaminated cream cakes with the virus. The sensitivity of electronmicroscopy and analyses of IgG antibodies in serum to detect the etiologic agent was very low. The sensitivity to Norwalk Virus Polymerase Chain Reaction was much higher, and this was a considerable diagnostic benefit during the epidemic. Close cooperation between the local health authorities, the food control authorities, the bakery and the public was necessary to diagnose the etiology, source and spread of this food-borne infection.

Anderson, A. D., V. D. Garrett, et al. (2001). "Multistate outbreak of Norwalk-like virus gastroenteritis associated with a common caterer." Am J Epidemiol 154(11): 1013-9.
	In February 2000, an outbreak of gastroenteritis occurred among employees of a car dealership in New York. The same meal was also supplied to 52 dealerships nationwide, and 13 states reported illness at dealerships where the banquet was served. A retrospective cohort study was conducted to identify risk factors associated with the illness. Stool samples were collected to detect Norwalk-like virus, and sera were drawn and tested for immunoglobulin A antibodies to the outbreak strain. By univariate analysis, illness was significantly associated with consumption of any of four salads served at the banquet (relative risk = 3.8, 95% confidence interval: 2.5, 5.6). Norwalk-like virus was detected by reverse transcription-polymerase chain reaction assay in 32 of 59 stool samples from eight states. Nucleotide sequences of a 213-base pair fragment from 16 stool specimens collected from cases in eight states were identical, confirming a common source outbreak. Two of 15 workers at caterer A had elevated immunoglobulin A titers to an antigenically related Norwalk-like virus strain. This study highlights the value of molecular techniques to complement classic epidemiologic methods in outbreak investigations and underscores the critical role of food handlers in the spread of foodborne disease associated with Norwalk-like virus.

Anderson, A. D., A. G. Heryford, et al. (2003). "A waterborne outbreak of Norwalk-like virus among snowmobilers-Wyoming, 2001." J Infect Dis 187(2): 303-6.
	In February 2001, episodes of acute gastroenteritis were reported to the Wyoming Department of Health from persons who had recently vacationed at a snowmobile lodge in Wyoming. A retrospective cohort study found a significant association between water consumption and illness, and testing identified Norwalk-like virus (NLV) in 8 of 13 stool samples and 1 well. Nucleotide sequences from the positive well-water specimen and 6 of the positive stool samples were identical. This multistrain NLV outbreak investigation illustrates the importance of NLV as a cause of waterborne illness and should encourage monitoring for NLVs in drinking water.

Anderson, C. E. (1957). "An infectious hepatitis outbreak in a country district." New Zealand Medical Journal 56: 235-237.
	
Anderson, D. A., A. G. Coulepis, et al. (1986). "Indirect immunofluorescence assay for the detection of hepatitis A virus-specific serum immunoglobulins." J Clin Microbiol 24(1): 163-5.
	Hepatitis A virus-specific BSC-1 cells were used for the detection of serum immunoglobulins to hepatitis A virus by indirect immunofluorescence. Of 150 serum samples tested, specific immunoglobulin M was detected only in patients with serologically confirmed acute hepatitis A, while specific immunoglobulin G was detected in patients with acute or past clinical hepatitis A as well as many patients with no known history of hepatitis.

Anderson, D. A. and B. C. Ross (1990). "Morphogenesis of hepatitis A virus: isolation and characterization of subviral particles." Journal of Virology 64(11): 5284-5289.
	The morphogenesis of hepatitis A virus (HAV) in BS-C-1 cells was examined by immunoblotting with antisera to capsid proteins and labeling of virus-specific proteins with L-[35S]methionine. Antiserum to VP2 detected two virus-specific proteins with apparent molecular masses of 30.6 and 30 kDa, representing VP0 and VP2, while antiserum to VP1 detected proteins with molecular masses of 33 and 40 kDa, representing VP1 and a virus-specific protein which we designated PX, respectively. Sedimentation of cell lysates revealed the presence of virions, procapsids, and pentamers, but particles analogous to the protomers of other picornaviruses were not detected. Although provirions and virions were not found as discrete species in our gradient system, it was evident that the rate of sedimentation was proportional to the relative amounts of VP0 and VP2 in particles, with slower-sedimenting particles (provirions) containing predominantly VP0 rather than VP2. Procapsids contained VP0 in addition to VP1 and VP3. Pentamers also contained VP0, but PX was present rather than VP1. These results suggest that PX is a precursor to VP1 and is most likely 1D2A. Primary cleavage of the viral polyprotein also occurs at the 2A-2B junction in cardioviruses and aphthoviruses, but assembly of pentamers containing 1D2A has not been reported for those viruses. The absence of detectable levels of protomers suggests a high efficiency of pentamer formation, which may be related to the high efficiency of viral RNA encapsidation for HAV (D.A. Anderson, B.C. Ross, and S.A. Locarnini, J. Virol. 62:4201-4206, 1988). The results of this study reveal further unusual aspects of the HAV replicative cycle which distinguish it from other picornaviruses and may contribute to its restricted replication in cell culture. 

Anderson, E. J. and S. G. Weber (2004). "Rotavirus infection in adults." Lancet Infect Dis 4(2): 91-9.
	Rotavirus has been recognised for 30 years as the most common cause of infectious gastroenteritis in infants and young children. By contrast, the role of rotavirus as a pathogen in adults has long been underappreciated. Spread by faecal-oral transmission, rotavirus infection in adults typically manifests with nausea, malaise, headache, abdominal cramping, diarrhoea, and fever. Infection can also be symptomless. Rotavirus infection in immunocompromised adults can have a variable course from symptomless to severe and sustained infection. Common epidemiological settings for rotavirus infection among adults include endemic disease, epidemic outbreak, travel-related infection, and disease resulting from child-to-adult transmission. Limited diagnostic and therapeutic alternatives are available for adults with suspected rotavirus infection. Because symptoms are generally self-limiting, supportive care is the rule. Clinicians caring for adults with gastroenteritis should consider rotavirus in the differential diagnosis. In this review we intend to familiarise clinicians who primarily provide care for adult patients with the salient features of rotavirus pathophysiology, clinical presentation, epidemiology, treatment, and prevention.

Anderson, O. (1921). "An epidemic of jaundice." Nordisk Hygienisk Tidskrift 2: 252.
	
Andino, R., N. Boddeker, et al. (1999). "Intracellular determinants of picornavirus replication." Trends Microbiol 7(2): 76-82.
	Viruses replicate in a restricted number of hosts and tissues. In addition to viral receptors, several intracellular factors can be involved in determining tissue tropism. Many proteins have recently been implicated in picornavirus translation and RNA replication. Although the functional role of these proteins has not been established in vivo, it is possible that they determine cell-type tropism and the pathogenic outcome of the infection.

Ando, T., Q. Jin, et al. (1995). "Epidemiologic applications of novel molecular methods to detect and differentiate small round structured viruses (Norwalk-like viruses)." Journal of Medical Virology 47(2): 145-152.
	The molecular epidemiology of a large, multistate outbreak of oyster-associated gastroenteritis [Kohn et al. (1995): Journal of the American Medical Association 273:466-471. Dowell et al. (1995): Journal of Infectious Diseases 171:1497-1503.] was examined using new methods to detect small round structured viruses (SRSVs) by reverse transcription-polymerase chain reaction (RT-PCR) and to characterize strains by Southern hybridization and nucleotide sequencing of 81-bp of a PCR product amplified from the RNA polymerase gene. Of 37 stool specimens examined from patients in eight clusters of the multistate outbreak, 32 (86%) gave RT-PCR products specific for SRSVs of P1-A phylogenetic group. Nineteen PCR products from the eight clusters were confirmed to have the identical sequence, indicating that this large outbreak was attributed to a single strain of SRSV. In one of the eight clusters, five (63%) of eight patients had a mixed infection with a second SRSV strain that belonged to P2-B phylogenetic group. Of 12 specimens from patients in five other outbreaks and one sporadic case which occurred at the same time as the multistate outbreak, 10 (83%) gave products specific for SRSVs representing four phylogenetic groups (P1-A, P1-B, P2-A, and P2-B). The sequences of the P1-A products from two outbreaks and that of the P2-B product from another outbreak were identical to the P1-A sequence from the eight clusters and the P2-B sequence from the one cluster of the multistate outbreak, respectively. These results demonstrate the first application of these methods to enhance our understanding of the molecular epidemiology of SRSVs and provide answers of public health interest that could not have been obtained using classical epidemiologic methods alone. 

Ando, T., S. S. Monroe, et al. (1995). "Detection and differentiation of antigenically distinct small round-structured viruses (Norwalk-like viruses) by reverse transcription-PCR and southern hybridization." J Clin Microbiol 33(1): 64-71.
	Application of reverse transcription (RT)-PCR to detect small round-structured viruses (SRSVs) from fecal specimens of patients with gastroenteritis has been insensitive because of the tremendous sequence heterogeneity between strains. We have designed two RT-PCR primer sets (G-1 and G-2) based on the nucleotide sequence diversity in the RNA polymerase gene of SRSVs belonging to two distinct genogroups represented by Norwalk virus (primers G-1) and Snow Mountain agent (primers G-2). All 22 SRSV strains examined that had been classified previously by solid-phase immune electron microscopy into four antigenic types (UK1, UK2, UK3, and UK4) could be detected by RT-PCR with these two primer sets. The G-1 primer set detected 6 UK2 strains, and the G-2 primers detected 16 strains, including 7 UK1, 5 UK3, and 4 UK4 strains. On the basis of nucleotide sequences of 81-bp fragments of the RT-PCR products from 13 strains determined in this study, together with those previously reported for 17 SRSV strains, we designed four sets of internal oligonucleotide probes (P1-A, P1-B, P2-A, and P2-B) for Southern hybridization, using chemiluminescent detection. The P1-A probe hybridized with PCR products from the UK2 strains; the P1-B probe, with products from two of the seven UK1 strains; the P2-A probe, with four of the remaining five UK1 strains; and the P2-B probe, with products from both UK3 and UK4 strains, as well as with one strain originally typed as UK1 which showed cross-reactivity with UK4 upon retesting by solid-phase immune electron microscopy. RT-PCR with both the G-1 and the G-2 primer sets can increase the detection rate of the many antigenically distinct SRSVs and, when combined with Southern hybridization, may predict the antigenic type of the SRSV associated with infection.

Ando, T., S. S. Monroe, et al. (1997). "A one-tube method of reverse transcription-PCR to efficiently amplify a 3-kilobase region from the RNA polymerase gene to the poly(A) tail of small round-structured viruses (Norwalk-like viruses)." J Clin Microbiol 35(3): 570-7.
	Amplification of a 3-kb genome region from the RNA polymerase gene to the 3' poly(A) tail of small round-structured virus (SRSV) by reverse transcription-PCR (RT-PCR) has been difficult to achieve because of a stable secondary structure in a region between the RNA polymerase gene and the 5' end of the second open reading frame. We have developed a one-tube RT-PCR method to efficiently amplify this region. The method comprises three procedures: purification of poly(A)+ RNA from a starting RNA solution by oligo(dT)30 covalently linked to latex particles, buffer exchange, and continuous RT and PCR in a single tube containing all reaction components. The key elements of this method are (i) first-strand cDNA synthesis with the Superscript II version of RNase H- Moloney murine leukemia virus reverse transcriptase at 50 degrees C for 10 min by using the RNA-oligo(dT)30 hybrid on the latex particles as the template and primer, and (ii) PCR by Taq and Pwo DNA polymerases mixed together with a mixture of 12 phased oligo(dT)25 antisense primers. The detection threshold of the one-tube RT-PCR method was as little as 0.2 ng of the crude RNA used as the source of the template. Using this method, we obtained 3-kb products from 24 SRSV strains previously characterized into four genetic groups. These included 5 P1-A, 4 P1-B, 5 P2-A, and 10 P2-B strains. Because SRSVs have not yet been cultivated in vitro, this novel method should facilitate molecular characterization of SRSVs to provide a firm scientific foundation for improvements and refinements of SRSV diagnostics.

Ando, T., M. N. Mulders, et al. (1994). "Comparison of the polymerase region of small round structured virus strains previously classified in three antigenic types by solid-phase immune electron microscopy." Archive of Virology 135(1-2): 217-226.
	We have used a reverse transcription-polymerase chain reaction with nested sets of primers to determine the nucleotide sequences of a 166 base pair segment of the RNA polymerase region of seven strains of small round structured viruses (SRSVs) from the United Kingdom. These SRSV strains were previously classified by solid-phase immune electron microscopy into three antigenic types--UK2, UK3 and UK4, which are comparable to the prototype strains Norwalk virus, Hawaii agent, and Snow Mountain agents, respectively. Based on their sequences, the seven strains from the United Kingdom could be divided into two groups. The first group included two strains of the UK2 type along with Norwalk virus and Southampton virus and the second group included three strains of UK3 and two strains of UK4 types. Viruses in the first group showed 75.3%-77.1% nucleotide and 89.1%-94.6% amino acid identity with Norwalk virus while those of the second group showed 60.8%-63.3% nucleotide and 67.3%-69.1% amino acid identity. Nucleotide and amino acid identity within the second group ranged between 91.6%-99.4% and 96.4%-100%, respectively. These results suggest that the SRSVs antigenically related with Norwalk virus, Hawaii agent, and Snow Mountain agent, can be classified into two genotypes on the basis of their sequences in the RNA polymerase region. 

Ando, T., J. S. Noel, et al. (2000). "Genetic classification of "Norwalk-like viruses." J Infect Dis 181 Suppl 2: S336-48.
	Reverse transcription-polymerase chain reaction has been used worldwide for the diagnosis of Norwalk-like virus (NLV) infection, yet a commonly accepted genetic classification scheme has not been established. Amino acid sequences from four regions of open-reading frame 2 (ORF2) were used to analyze 101 NLV strains, including 2 bovine strains. On the basis of this analysis, a genetic classification scheme is proposed that differentiates 99 human strains into 2 major genetic groups consisting of 5 and 10 genetic clusters, respectively. The 2 bovine strains constitute a newly defined third major genetic group composed of 2 putative clusters represented by each strain. This classification scheme is well supported by the analysis of the entire ORF2 sequences from 38 strains selected to represent the genetic diversity of the human strains used above. This scheme should provide a firm scientific basis for the unified classification of NLV strains detected around the world.

Andreoletti, L., D. Hober, et al. (1997). "Experimental CVB3-induced chronic myocarditis in two murine strains: evidence of interrelationships between virus replication and myocardial damage in persistent cardiac infection." Journal of Medical Virology 52(2): 206-214.
	In order to analyse the relationships between enteroviral replication and the myocardial damage at the onset of chronic cardiac infection, 2 mouse strains with different degrees of immunological competence (NMRI nu/nu, DBA/2) were infected by a myocarditic Coxsackie virus B3 (CVB3-M1) variant. At 31 days post-inoculation, plaque-forming assay, polymerase chain reaction (RT-PCR), and immunohistochemistry were carried out for detecting viruses and viral components in the myocardium. The virological findings were related to histopathological changes in the myocardium as well to the dilatation of both cardiac ventricles. Chronic myocardial lesions characterized by large fibrosis areas and interstitial inflammatory infiltrates were detected together with cardiomegalia in 52.6% (10/19) of athymic mice and in 9% (2/22) of euthymic mice. Viral replication foci were located and were found only in myocarditic cells adjacent to myocardial inflammatory lesions by immunostaining myocardial tissue sections with anti-serum to VP1 virus capsid protein. Using PCR followed by microwell capture hybridization assay, a large excess of viral positive strand RNA over negative strand was semiquantified in heart tissue from mice with chronic myocarditis, whereas approximately equal amounts of plus and minus strand RNA were detected in cases of persistent cardiac infection without chronic myocardial injuries. These findings provide evidence of the major role of viral replication in the pathogenesis of chronic murine CVB3-induced cardiomyopathy. The results indicate that the cardiac persistence of enteroviral RNAs can be observed without chronic cardiomyopathy, which could be explained by a defective viral positive RNA replication. 

Andreoletti, L., D. Hober, et al. (1996). "Rapid detection of enterovirus in clinical specimens using PCR and microwell capture hybridization assay." Journal of Virological Methods 62(1): 1-10.
	A rapid detection method of enteroviral RNA in clinical samples using PCR and a microwell capture hybridization assay is described. PCR products were labelled directly by digoxigenin-dUTP during the amplification step. The labelled amplicons were hybridized with a biotinylated oligo-probe and captured on commercially available test microwells coated with streptavidin. The hybridized amplicons labelled with digoxigenin were detected using anti-digoxigenin Fab fragments conjugated to peroxidase and colorimetric reaction automatically measured. This method detected as few as 0.01 PFU/100 microl of biological sample with a result obtained within 8 h. Using this method, we were able to detect enteroviral RNA in 23 of 35 clinical specimens from 16 of 17 patients with suspected acute or chronic enteroviral infection. The samples included cerebrospinal fluid, broncho-pulmonary lavage, pericardial effusion, throat swabs, stools, sera, muscular and myocardial biopsies. In contrast, virus was isolated in cell culture in only 8 of 28 clinical specimens from 6 of the 17 patients. This easy-to-perform assay has useful potential in the rapid detection of enterovirus in acute or chronic infection. This methodology could be used for a rapid qualitative detection of other RNA viruses. 

Andreoletti, O., P. Berthon, et al. (2000). "Early accumulation of PrP(Sc) in gut-associated lymphoid and nervous tissues of susceptible sheep from a Romanov flock with natural scrapie." J Gen Virol 81(Pt 12): 3115-26.
	The immune system is known to be involved in the early phase of scrapie pathogenesis. However, the infection route of naturally occurring scrapie and its spread within the host are not entirely known. In this study, the pathogenesis of scrapie was investigated in sheep of three PrP genotypes, from 2 to 9 months of age, which were born and raised together in a naturally scrapie-affected Romanov flock. The kinetics of PrP(Sc) accumulation in sheep organs were determined by immunohistochemistry. PrP(Sc) was detected only in susceptible VRQ/VRQ sheep, from 2 months of age, with an apparent entry site at the ileal Peyer's patch as well as its draining mesenteric lymph node. At the cellular level, PrP(Sc) deposits were associated with CD68-positive cells of the dome area and B follicles before being detected in follicular dendritic cells. In 3- to 6-month-old sheep, PrP(Sc) was detected in most of the gut-associated lymphoid tissues (GALT) and to a lesser extent in more systemic lymphoid formations such as the spleen or the mediastinal lymph node. All secondary lymphoid organs showed a similar intensity of PrP(Sc)-immunolabelling at 9 months of age. At this time-point, PrP(Sc) was also detected in the autonomic myenteric nervous plexus and in the nucleus parasympathicus nervi X of the brain stem. These data suggest that natural scrapie infection occurs by the oral route via infection of the Peyer's patches followed by replication in the GALT. It may then spread to the central nervous system through the autonomic nervous fibres innervating the digestive tract.

Andreoletti, O., C. Lacroux, et al. (2002). "PrP(Sc) accumulation in placentas of ewes exposed to natural scrapie: influence of foetal PrP genotype and effect on ewe-to-lamb transmission." J Gen Virol 83(Pt 10): 2607-16.
	Placentas from scrapie-affected ewes are known to be infectious. Nevertheless, placenta infectivity in such ewes is not systematic. Maternal transmission to lambs is highly suspected but contamination of the foetus in utero has not been demonstrated. Using ewes from a naturally scrapie-infected flock, it was demonstrated that abnormal prion protein (PrP(Sc)) accumulation in the placenta (i) is controlled by polymorphisms at codons 136, 154 and 171 of the foetal PrP gene and (ii) is restricted mainly to placentome foetal trophoblastic cells. In order to go deeper into the role of the placenta in scrapie transmission, the pattern of PrP(Sc) dissemination was established in susceptible lambs (genotype VRQ/VRQ) sampled from 140 days post-insemination to the age of 4 months from either VRQ/VRQ ewes with PrP(Sc)-positive placentas or ARR/VRQ ewes with PrP(Sc)-negative placentas. In both VRQ/VRQ lamb groups, PrP(Sc) spatial and temporal accumulation patterns were similar, suggesting post-natal rather than in utero contamination.

Andries, K., B. Rombaut, et al. (1994). "Discrepancy between infectivity and antigenicity stabilization of oral poliovirus vaccine by a capsid-binding compound." J Virol 68(5): 3397-400.
	Two hundred forty pyridazinamine derivatives were tested for the ability to stabilize the antigenicity and infectivity of oral poliovirus vaccine subjected to 45 degrees C for 2 h. Seven compounds stabilized the antigenicity of all three vaccine strains and neutralized the viral particles in a way that is reversible by dilution. Of these, R 77975 (pirodavir) was selected for vaccine potency tests. Sabin type 2 and type 3 strains were subjected to 4, 25, 42, and 45 degrees C for 1 week in the presence and absence of R 77975. Although R 77975 particularly stabilized the infectivity of the most thermolabile vaccine strain (Sabin type 3), the protection did not exceed that of 1 M MgCl2. When virus was inactivated in the absence of R 77975, the native or N antigenicity changed in H antigenicity. However, in the presence of the capsid-binding compound, N antigenicity was preserved in particles that had lost infectivity.

Ang, L. H. (1998). "An outbreak of viral gastroenteritis associated with eating raw oysters." Commun Dis Public Health 1(1): 38-40.
	Nine members of a party of 24 people who attended a birthday party fell ill with gastroenteritis between one and three days later. A cohort study undertaken using a postal questionnaire showed that illness was associated with having eaten raw oysters. Six of the cases had their stools examined and two were positive for small round structured virus. The illness was brief and none of the cases had consulted a general practitioner. Had the cases not been part of a party they would not have been identified. The oysters were grown in English coastal waters in grade B oyster beds. They underwent depuration treatment before they were sold for consumption. More work is needed to protect oyster beds from contamination and to identify methods to render oysters safe for consumption.

Anonymous (1988). "Outbreak of hepatitis A--Shanghai." WHO Weekly Epidemiology Records 63(13): 91-2.
	
Anonymous (1990). "Food poisoning outbreak linked to Sydney rock oysters." WHO Surveillance Programme for Control of Foodborne Infections and Intoxications in Europe 3.
	
Anonymous (1990). "Foodborne disease surveillance in England and Wales: 1986-1988.  Part 1. Trends in reporting cases and outbreaks of food poisoning and salmonellosis." Communicable Disease Report, London 90(15): 3-6.
	
Anonymous (1990). "Foodborne disease surveillance in England and Wales: 1986-1988. Part 2. Review of agents causing foodborne illness." Communicable Disease Report, London 90(19): 3-6.
	
Anonymous (1991). "Outbreak of diarrhoeal illness associated with coronovirus infection." Communicable Disease and Environmental Health Weekly Report, Scotland 25(46): 1.
	
Anonymous (1993). "Foodhandlers implicated in Denver hepatitis outbreak." Food Protection Report 9(1): 1-3.
	
Anonymous (1993). "Gastrointestinal virus infections, England and Wales: laboratory reports, weeks 92/52-93/01." Communicable Disease Report 3(3): 10.
	
Anonymous (1994). "Hepatitis A Vaccine: "Havrix Monodose"." Communicable Disease and Environmental Health: Scotland Weekly Report 28(94/21): 3.
	
Anonymous (1994). "Outbreak of tick-borne encephalitis, presumably milk-borne." Weekly Epidemiology Research 69(13): 140-141.
	
anonymous (1998). "Outbreaks of gastroenteritis in England and Wales associated with shellfish: 1996 and 1997." Communicable Disease Report CDR Weekly 8: 21-24.
	
Ansari, S. A., S. R. Farrah, et al. (1992). "Presence of human immunodeficiency virus nucleic acids in wastewater and their detection by polymerase chain reaction." Applied and Environmental Microbiology 58(12): 3984-3990.
	The human immunodeficiency virus type 1 (HIV-1) released by infected individuals or present in human and hospital wastes can potentially cause contamination problems. The presence of HIV-1 was investigated in 16 environmental samples, including raw wastewater, sludge, final effluent, soil, and pond water, collected from different locations. A method was developed to extract total nucleic acids in intact form directly from the raw samples or from the viral concentrates of the raw samples. The isolated nucleic acids were analyzed for the presence of HIV-1 by using in vitro amplification of the target sequences by the polymerase chain reaction (PCR) method. HIV-1-specific proviral DNA and viral RNA were detected in the extracted nucleic acids obtained from three wastewater samples by this method. The specificity of the PCR-amplified products was determined by Southern blot hybridization with an HIV-1-specific oligonucleotide probe, SK19. The isolated nucleic acids from wastewater samples were also screened for the presence of poliovirus type 1, representing a commonly found enteric virus, and simian immunodeficiency virus, representing, presumably, rare viruses. While poliovirus type 1 viral RNA was found in all of the wastewater samples, none of the samples yielded a simian immunodeficiency virus-specific product. No PCR-amplified product was yielded when wastewater samples were directly used for the detection of HIV-1 and poliovirus type 1. The wastewater constituents appeared to be inhibitory to the enzymes reverse transcriptase and DNA polymerase. 

Ansari, S. A., S. A. Sattar, et al. (1988). "Rotavirus survival on human hands and transfer of infectious virus to animate and nonporous inanimate surfaces." J Clin Microbiol 26(8): 1513-8.
	We tested the survival of the Wa strain of human rotavirus on the hands of volunteers and also studied infectious virus transfer between animate and inanimate (stainless steel disks) surfaces. The virus was diluted in a 10% suspension of feces, and 10 microliters (1 X 10(3) to 4 X 10(4) PFU) was placed on each of the four fingerpads of the left hand. One milliliter of 20% tryptose phosphate broth in Earle balanced salt solution was used for virus elution from each fingerpad, and the hands were disinfected with 70% ethanol before they were washed with an antiseptic soap and water. At 20, 60, and 260 min after inoculation, approximately 57, 43, and 7%, respectively, of the input infectious virus could be recovered. For virus transfer, the inoculum (2 X 10(4) to 8 X 10(4) PFU) was allowed to dry, and the donor surface was kept in contact with the recipient surface for 10 s at a pressure of approximately 1 kg/cm2. At 20 and 60 min after virus inoculation, 16.1 and 1.8%, respectively, of the input infectious virus could be transferred from the contaminated hand to a clean disk; when a clean hand was pressed against a contaminated disk, virus transfer was 16.8 and 1.6%, respectively. Contact between a contaminated and a clean hand 20 and 60 min after virus inoculation resulted in the transfer of 6.6 and 2.8%, respectively, of the input infectious virus. These findings indicate the potential vehicular role for human hands in the spread of rotaviral infections.

Ansari, S. A., S. A. Sattar, et al. (1989). "In vivo protocol for testing efficacy of hand-washing agents against viruses and bacteria: experiments with rotavirus and Escherichia coli." Appl Environ Microbiol 55(12): 3113-8.
	Ten antiseptic formulations, an unmedicated liquid soap, and tap water alone were compared for their capacities to eliminate human rotavirus from the finger pads of adult volunteers; three of the antiseptics, the soap, and the tap water alone were also tested against Escherichia coli. A fecal suspension of virus or bacterium was placed on each finger pad and air dried. The contaminated site was exposed to the test product for 10 s, rinsed in tap water, and dried on a paper towel. The residual virus or bacterium was then eluted. Selected agents were also tested by an analogous whole-hand method by which the entire palm surfaces of both hands were contaminated. Alcohols (70%) alone or with Savlon reduced the virus titer by greater than 99%, whereas the reductions by Proviodine, Dettol, and Hibisol ranged from 95 to 97%. Aqueous solutions of chlorhexidine gluconate were significantly less effective for virus removal or inactivation than 70% alcohol solutions. Furthermore, Savlon in water (1:200) was found to be much less effective in eliminating the virus (80.6%) than the bacterium (98.9%). The tap water alone and the soap reduced the virus titers by 83.6 and 72.5% and the bacterial titers by 90 and 68.7%, respectively. The results of the whole-hand method agreed well with those of the finger pad protocol. We conclude that the finger pad method is a suitable model for testing the in vivo efficacy of hand-washing agents and emphasize the need for using appropriate test viruses and bacteria.

Ansari, S. A., V. S. Springthorpe, et al. (1991). "Survival and vehicular spread of human rotaviruses: possible relation to seasonality of outbreaks." Reviews of Infectious Diseases 13(3): 448-461.
	In developing countries rotavirus infections account for nearly 6% of all diarrheal episodes and for 20% of diarrhea-associated deaths of young children. Even in industrialized countries rotavirus diarrhea in the young is among the leading causes of hospitalization. In temperate regions institutional outbreaks of the disease occur mainly in cold dry weather, whereas in tropical settings the seasonality is less well defined. Waterborne outbreaks of rotavirus gastroenteritis have been recorded; air, hands, fomities, and food may also act as vehicles for this infection. Rotaviruses can survive for weeks in potable and recreational waters and for at least 4 hours on human hands. In air and on nonporous inanimate surfaces, the survival of rotaviruses is favored by a relative humidity of less than or equal to 50% and viral infectivity can be retained for several days. Rotaviruses are relatively resistant to commonly used hard-surface disinfectants and hygienic hand-wash agents. 

Apaire-Marchais, V., V. Ferre-Aubineau, et al. (1994). "Development of RT-semi-nested PCR for detection of hepatitis A virus in stool in epidemic conditions." Molecular and Cellular Probes 8(2): 117-124.
	The purpose of this study was to determine the efficiency of semi-nested PCR in detecting hepatitis A virus (HAV) RNA. During a 2-year period (1990-1991), HAV RNA was searched for in shellfish from the French Brittany coasts using cRNA and vRNA probes. In January 1992, at the time of a hepatitis A outbreak, 28 stool samples were collected from infected patients (18 adults, 10 children) with anti-HAV IgM. Four samples from subjects with negative HAV serology were used as negative controls. Nucleic acid amplification (reverse-transcription-semi-nested PCR) was performed to detect HAV in stool. HAV RNA was purified by phenol-chloroform extraction and converted to cDNA using reverse transcriptase (Mu-MLV). After amplification, PCR products were visualized on an ethidium-bromide-stained gel and confirmed by hybridization with a specific digoxigenin-labelled oligoprobe. Samples were also studied by molecular hybridization with cRNA and vRNA probes. After onset of the illness, HAV RNA was detected over a longer time period by semi-nested PCR (16/28) than by hybridization (0/28). Even though biological diagnosis of hepatitis A will continue to rely on the detection of anti-HAV IgM, PCR should be useful in certain clinical cases (diagnosis of relapse) and for epidemiological and environmental monitoring of viruses. 

Apaire-Marchais, V., B. H. Robertson, et al. (1995). "Direct sequencing of hepatitis A virus strains isolated during an epidemic in France." Applied and Environmental Microbiology 61(11): 3977-3980.
	Direct sequencing of PCR products was used to study the VP1 region of the hepatitis A virus (HAV) genome (position 2199 to 2356) of nine strains isolated from human stools collected during a hepatitis A epidemic (western France, 1992), three strains from environmental samples (1990, 1991, and 1992), and two HAV cell culture isolates (the French strain CF53/Lyon and strain CLF). These viruses differed from CF53/Lyon (genotype I) by between 1 and 10.3%, and results indicated the existence of two groups of strains belonging to two different subgenotypes (IA and IB). With this sequencing technique it was possible to monitor the epidemiology of HAV and study its relations. 

Appleton, H. (1987). "Small round viruses: classification and role in food-borne infections." Ciba Found Symp 128: 108-25.
	Since the first observation of Norwalk virus in the electron microscope in 1972, many different small virus particles in the size range 20-40 nm have been described world-wide in association with outbreaks of gastroenteritis. Progress characterizing these agents has been hampered by the relatively small numbers of particles present in clinical material and the lack of success in culturing them. Although the relationship between some of these viruses remains confusing, a number of distinct groups has emerged, based on morphological features and limited physical data. Immuno-electron microscopy has proved valuable in detecting viruses but the addition of antibody can mask surface morphological features. Examination of viruses in negatively stained preparations without added antibody has revealed distinct morphological differences and viruses previously thought to be simply antigenic variants within the Norwalk group of viruses clearly belong to other groups. Preliminary evidence suggests that one human virus unrelated to Norwalk has a single-stranded DNA genome and is a parvovirus. Some groups have been implicated in outbreaks of food-borne gastroenteritis, particularly after the consumption of shellfish, and their role in other food-borne and water-borne outbreaks is being increasingly recognized.

Appleton, H. (1990). "Foodborne illness: foodborne viruses." Lancet 336(8727): 1362-1364.
	not available

Appleton, H. (1990). "Laboratory investigations of viral gastroenteritis." Communicable Disease Report, London 90(43): 5.
	
Appleton, H. (1991). Hepatitis. Public Health Aspects of Seafood-Borne Zoonotic Diseases. E. M. E. V. H. R. v. O.-I. Bernoth. 1: 109-116.
	
Appleton, H. (1994). Norwalk Virus and the Small Round Viruses Causing Foodborne Gastroenteritis. Foodborne Disease Handbook: Vol. 2. Diseases Caused by Viruses, Parasites, and Fungi. Y. H. Hui, J. R. Gorham, K. D. Murrell and D. O. E. Cliver. New York, Marcel Dekker, Inc. 2: 57-79.
	
Appleton, H. (2000). "Control of food-borne viruses." Br Med Bull 56(1): 172-83.
	There are two main food-borne virus infections. These are viral gastroenteritis caused by small round structured viruses (SRSV) of the Norwalk group and hepatitis A. Both infections are normally transmitted directly from person-to-person, but on occasions they may also be food-borne or water-borne. Viruses do not multiply or produce toxins in foods, and foods merely act as vehicles for their passive transfer. Foods may be contaminated by infected food-handlers, and outbreaks frequently involve cold foods that require much handling during preparation. Foods may also be contaminated in their growing and harvesting areas by sewage polluted water, and molluscan shellfish have been particularly implicated. PCR and ELISA based methods are being developed for detection and typing of viruses in patients and also in food samples. Sensitive detection methods should facilitate the design of improved food processing methods to ensure virus-free food.

Appleton, H., S. R. Palmer, et al. (1981). "Foodborne gastroenteritis of unknown aetiology: a virus infection?" Br. Med. J. 282(6278): 1801-1802.
	In almost a quarter of outbreaks of gastroenteritis reported to the Public Health Laboratory service by medical officers of environmental health and environmental health officers as possible foodborne infection in 1980 food poisoning organisms were not isolated. In a third of this group the incubation period was longer than the usual range for bacterial food poisoning organisms, and possibly some of the outbreaks were viral in origin. Viruses were detected by electron microsocpy in 88% of faecal specimens from similar outbreaks associated with shellfish but in only 23% of specimens from outbreaks associated with other foods. Recommendations are made for future investigation of such outbreaks including the collection of epidemiological data and specimens for virological study.

Appleton, H. and M. S. Pereira (1977). "A possible virus aetiology in outbreaks of food-poisoning from cockles." Lancet 1(8015): 780-1.
	In a series of outbreaks of food-poisoning associated with the consumption of cockles, no bacterial pathogens were demonstrable either in faeces of patients or in cockles. However, small round virus-like particles have been detected in a high proportion of the faecal specimens in three of the outbreaks. These particles are similar in size, morphological features and density to particles seen in outbreaks of winter vomiting and non-bacterial gastroenteritis although in preliminary tests they are serologically distinctive.

Arankalle, V. A. and K. Banerjee (1995). "Hepatitis A infection." Med Hypotheses 44(3): 227-8.
	
Arankalle, V. A., M. S. Chadha, et al. (2001). "Changing epidemiology of hepatitis A and hepatitis E in urban and rural India (1982-98)." J Viral Hepat 8(4): 293-303.
	The epidemiology of hepatitis A virus (HAV) and hepatitis E virus (HEV) was assessed among age-stratified urban high socioeconomic, lower middle socioeconomic status and rural populations from western India in 1998. When compared with previous surveys, a clear shift from high to intermediate endemicity of HAV was evident only for higher socioeconomic population (1982-98), raising the possibility of outbreaks of hepatitis A in this category. A decrease in anti-HAV positivity was noted in rural children aged 6-10 years. Lower circulation of HEV was noted among < 25-year-old urban higher socioeconomic and rural individuals. For both viruses, the lower middle socioeconomic populations were comparable in 1982 and 1998. Socioeconomic status and family size (odds ratio = 23 and 1.6, respectively) were independently associated with anti-HAV positivity. Age, lower middle socioeconomic status and well water were significant independent variables for HEV infection (odds ratio = 5.7, 2.4 and 1.9, respectively). Hence, vaccination policy for hepatitis A needs to be reviewed.

Arankalle, V. A., M. S. Chadha, et al. (1995). "Cross-challenge studies in rhesus monkeys employing different Indian isolates of hepatitis E virus." J Med Virol 46(4): 358-63.
	The aim of this study was to determine if rhesus monkeys infected with one isolate of hepatitis E virus (HEV) were immune to subsequent challenge with other isolates of the virus. Three epidemic and one sporadic Indian HEV isolates were employed in the study. The interval between primary inoculation and challenge varied from 1 year and 6 months to 2 years and 9 months. Evidence of HEV infection was ascertained by rise in serum alanine transaminase (ALT) levels and/or seroconversion to antibodies to HEV (anti-HEV), and the presence of HEV-RNA in the bile or faeces of the infected monkeys. No evidence for multiplication of virus in monkeys challenged with different HEV isolates was obtained. These results show that immunity generated by one isolate of HEV protects against different isolates of hepatitis E virus.

Arankalle, V. A., M. S. Chadha, et al. (1988). "Outbreak of enterically transmitted non-A, non-B hepatitis among schoolchildren." Lancet 2(8621): 1199-200.
	
Arankalle, V. A., M. S. Chadha, et al. (1994). "Seroepidemiology of water-borne hepatitis in India and evidence for a third enterically-transmitted hepatitis agent." Proc. Natl. Acad. Sci. U S A 91(8): 3428-3432.
	Many epidemics of water-borne hepatitis have occurred throughout India. These were thought to be epidemics of hepatitis A until 1980, when evidence for an enterically transmitted non-A, non-B hepatitis was first reported. Subsequently, hepatitis E virus was discovered and most recent epidemics of enterically transmitted non-A, non-B hepatitis have been attributed to hepatitis E virus infection. However, only a limited number of cases have been confirmed by immuno electron microscopy, polymerase chain reaction, or seroconversion. In the present study we have performed a retrospective seroepidemiologic study of 17 epidemics of water-borne hepatitis in India. We have confirmed that 16 of the 17 epidemics were caused at least in part by serologically closely related hepatitis E viruses. However, one epidemic, in the Andaman Islands, and possibly a significant minority of cases in other epidemics, appears to have been caused by a previously unrecognized hepatitis agent.

Arankalle, V. A., L. P. Chobe, et al. (2002). "Human and swine hepatitis E viruses from Western India belong to different genotypes." J. Hepatol. 36(3): 417-425.
	BACKGROUND/AIMS: Hepatitis E is endemic in India. Earlier, we showed prevalence of IgG antibodies to hepatitis E virus (IgG-anti-HEV) in different animal species and inability of at least one human hepatitis E virus (HEV) strain to infect pigs. In the US where hepatitis E is not endemic in humans, zoonotic spread of HEV was suspected as swine and human HEV were closely related and cross-species infection was documented. The present study attempts to identify and partially characterize swine HEV from India. METHODS: Serum samples from 284 pigs were screened for the presence of HEV-RNA (nested polymerase chain reaction; PCR) and IgG-anti-HEV (enzyme-linked immunosorbent assay; ELISA). PCR products (Open Reading Frame-2 region) were sequenced and subjected to phylogenetic analysis. Two sero-negative pigs were inoculated with swine HEV-positive serum pool. RESULTS: ELISA and PCR positivity were 42.9 and 4.6%, respectively. All Indian swine HEV sequences clustered with genotype IV. Pigs could be experimentally infected with swine HEV. CONCLUSIONS: Swine HEV circulates in Indian pigs. In contrast to US and Taiwan wherein both human and swine HEV isolates belong to same genotype, Indian human HEV isolates belong to genotype I whereas genotype IV circulates in swine. Though experimental infection with Indian swine HEV was possible, at least one human HEV strain could not infect pigs.

Arankalle, V. A., J. Jha, et al. (1995). "Contribution of HEV and HCV in causing fulminant non-A, non-B hepatitis in western India." J Viral Hepat 2(4): 189-93.
	During 1990, 38 patients with fulminant non-A, non-B hepatitis (NANB) died in Government Medical College Hospital, Aurangabad. Serum samples from these patients were tested for antibodies to hepatitis C virus (anti-HCV) and IgM antibodies to hepatitis E virus (IgM-anti-HEV). All samples were also subjected to polymerase chain reaction (PCR) for the detection of HBV DNA, HCV RNA and HEV RNA. None of the patients had circulating anti-HCV antibodies; three had HCV RNA. Based on anti-HEV-IgM positivity 14 patients (37%) could be diagnosed as suffering from hepatitis E. None was positive for HEV RNA. In the absence of serological markers, HBV DNA was present in three cases. None of the HBV DNA positive patients had anti-delta antibodies. Dual infections (HBV with HEV, and HBV with HCV) were seen in two cases. The aetiology of half of the NANB cases could not be assigned to the known hepatitis viruses using current techniques.

Arankalle, V. A., M. V. Joshi, et al. (2001). "Prevalence of anti-hepatitis E virus antibodies in different Indian animal species." J Viral Hepat 8(3): 223-7.
	Prevalence of IgG antibodies to hepatitis E virus (IgG-anti-HEV) was determined among different animal species from India. Seropositivity varied from 4.4% to 6.9% in cattle, 54.6-74.4% in pigs and 2.1-21.5% in rodents. Of the 44 dogs screened, 10 were positive (22.7%). None of the 250 goat sera tested were found to be anti-HEV positive. Among rodents, over 50% serum samples collected in 1985 from Bandicota bengalensis were positive for anti-HEV antibodies. No evidence of HEV infection was obtained following experimental inoculation of an Indian strain (AKL-90) of HEV into anti-HEV negative pigs and goats. The results document varied prevalence of anti-HEV antibodies in different animal species from India and of inability of Indian pigs and goats to support replication of at least one human strain of HEV.

Arankalle, V. A., J. Ticehurst, et al. (1988). "Aetiological association of a virus-like particle with enterically transmitted non-A, non-B hepatitis." Lancet 1(8585): 550-4.
	Virus-like particles, approximately 27 nm in diameter, were identified in faeces from an Indian patient with enterically transmitted non-A, non-B (ENANB) hepatitis. They were serologically distinct from hepatitis A virus (HAV). Nucleic acid extracted from the particles did not hybridize with cDNA probes representing the genomes of HAV, enteroviruses, and cardioviruses. Chimpanzees were experimentally inoculated with faecal suspensions containing this 27 nm particle or with faeces from another case of ENANB hepatitis. Mild histological and biochemical hepatitis developed in these animals and there was serological evidence of infection with the virus-like particle as shown by immunoelectronmicroscopy (IEM). Serological analysis by IEM suggested that this agent or an antigenically similar virus was the aetiological agent of two epidemics and a sporadic case of ENANB hepatitis in India and of an epidemic of the illness in the USSR. Antibody to the particle was found in sera from patients with ENANB hepatitis from various geographic areas over a 30-year period.

Arankalle, V. A., S. A. Tsarev, et al. (1995). "Age-specific prevalence of antibodies to hepatitis A and E viruses in Pune, India, 1982 and 1992." J Infect Dis 171(2): 447-50.
	The age-specific seroprevalence of antibody to hepatitis A virus (HAV) and antibody to hepatitis E virus (HEV) were studied in persons in Pune, India, where both viruses are endemic. The data showed that HAV infected the majority of persons by age 3 years and virtually 100% by late childhood. In contrast, infection with HEV was rare in children and did not reach peak prevalence (33%-40%) until early adulthood. The reason for the differences in infection rates between HAV and HEV is not known. Age-specific antibody patterns in serum samples obtained 10 years apart show that neither HAV nor HEV has diminished in medical importance in this Indian community.

Araujo, R. M., A. Puig, et al. (1997). "Phages of enteric bacteria in fresh water with different levels of faecal pollution." J Appl Microbiol 82(3): 281-6.
	Levels of somatic and F-specific coliphages, and phages infecting Bacteroides fragilis were measured in 257 samples collected in different freshwater environments with different levels and characteristics of faecal pollution. In samples with recent pollution of domestic origin, the numbers of the three groups of phages were highly correlated, thus showing that their excretion is fairly constant. In this set of samples somatic coliphages, which were the most abundant, and F-specific coliphages outnumbered significantly Bact. fragilis phages. Normalized lines of the numbers of the three groups of phages in water samples and their sediments show that they settle similarly. The correlation between the values of the three groups of phages was not observed in waters with intermediate levels of pollution. An increase in the relative numbers of coliphages with respect to numbers of phages infecting Bact. fragilis was observed. In waters with persistent faecal pollution a dramatic change was recorded in the relative numbers of the different groups of phages. Phages infecting Bact. fragilis suffered the lowest reduction in numbers.

Archer, T. C. R. (1954). "An epidemic of infectious hepatitis apparently due to a water-borne agent." Journal of the Royal Army Medical Corps 100: 161-170.
	
Arlinghaus, R. B., J. Polatnick, et al. (1966). "Studies on foot-and-mouth disease virus ribonucleic acid synthesis." Virology 30(3): 541-50.
	
Armigliato, M., F. Bortolotti, et al. (1986). "Epidemiology of hepatitis A in northern Italy: A seven-year survey." Infection 14(6): 283-285.
	During a seven-year survey of acute symptomatic viral hepatitis in Padua (Northern Italy), the epidemiological features of hepatitis A were evaluated in 207 consecutive patients (120 males, mean age 22.7 .plus-minus. 11.4 years). The annual attack rate of the disease decreased significantly (p < 0.05) between 1978 and 1979 (0.11/1000 inhabitants) and 1981 and 1984 (0.04-0.03/1000 inhabitants), mainly due to its declining prevalence in the pediatric age. In parallel with the shifting of hepatitis A towards adulthood, single sources of infection, mainly associated with adult life-style such as foreign travel and raw shellfish ingestion, have become more and more prominent. The spread of drug abuse has not influenced the epidemiology of hepatitis A in our area.

Armon, R., R. Araujo, et al. (1997). "Bacteriophages of enteric bacteria in drinking water, comparison of their distribution in two countries." J Appl Microbiol 83(5): 627-33.
	The presence of bacteriophages infecting enteric bacteria was tested in more than 1500 drinking water samples in Israel and Spain. Bacteriophages tested were somatic coliphages, F-specific bacteriophages and Bacteroides fragilis bacteriophages. The three groups of bacteriophage were isolated in 100 ml water samples by the presence/absence test with similar frequencies, which ranged from 4.4% for somatic coliphages to 6.1% for bacteriophages infecting Bact. fragilis. In contrast, the frequency of isolation of bacteriophages was significantly higher than the frequency of isolation of faecal coliforms, which averaged only 1.9%. No significant differences were observed between the frequencies of isolation between the samples tested in Spain and those tested in Israel. The percentage of groundwater samples containing faecal coliforms and somatic coliphages was reduced significantly by chlorination, despite known deficiencies. However, there was no effect on the occurrence of F-specific bacteriophages and Bact. fragilis bacteriophages.

Armson, A., B. P. Meloni, et al. (1999). "Assessment of drugs against Cryptosporidium parvum using a simple in vitro screening method." FEMS Microbiology Letters 178(2): 227-233.
	A rapid semi-quantitative screening method was devised for assessing the anticryptosporidial and cytotoxic effects of putative chemotherapeutic compounds. The method is suitable as an initial rapid screening procedure from which compounds demonstrating anticryptosporidial activity can be identified for further analysis. It has the advantages of speed, low cost and concurrent assessment of anticryptosporidial and cytotoxic effects and allows accurate determination of minimum lethal concentrations. Of the 71 compounds screened, six completely inhibited cryptosporidial growth at 1 microM (monensin, salinomycin, alborixin, lasalocid, trifluralin and nicarbazin) and a further eight showed significant anticryptosporidial activity at 1 or 20 microM (halquinol, bleomycin, suramin, mitomycin, doxycycline hydrochloride, toltrazuril, chloroquine phosphate and teniposide). Twelve compounds were found to have some degree of cytotoxicity at 1 microM and a further 12 at 20 microM. 

Arnal, C., J. M. Crance, et al. (1998). "Persistence of infectious hepatitis A virus and its genome in artificial seawater." Zentralbl Hyg Umweltmed 201(3): 279-84.
	The stability of the hepatitis A virus (HAV) genome detectable by RT- PCR in artificial sterile seawater seeded with HAV has been compared to that of HAV detectable in cell culture. The HAV genome was detectable by RT-PCR for 232 days while virus particles were detectable in cell culture for only 35 days. This difference in stability indicates that detection of the HAV genome by RT-PCR is not a reliable indicator of the survival of HAV detectable in cell cultures. However, before these results can be extrapolated to stability in natural seawater, the effect of additional elements in the natural environment, such as bacteria, fungi and suspended matter, on the stability of the HAV genome and cell culture infectious HAV particles, will have to be examined.

Arnal, C., V. Ferre-Aubineau, et al. (1998). "Simplified reverse transcription polymerase chain reaction procedure with detection by microplate hybridization for routine screening of hepatitis A virus." Can J Microbiol 44(3): 298-302.
	Reverse transcription polymerase chain reaction, using either nested or seminested primers, is used extensively for the detection of viruses in small quantities. However, existing methods are prone to false positive reactions. We report here an improved polymerase chain reaction technique based on the use of longer primers (39 nucleotides) with single-step amplification, applied to the detection of hepatitis A in low quantities. While the sensitivity of this technique (10 x the 50% tissue culture infective dose) is equivalent to that of existing methods, it is a simpler procedure, less time consuming, and less susceptible to contamination and therefore provides a more reliable tool for routine diagnosis. Finally, the development of a DNA enzyme immunoassay detection technique and the complete automation of the procedure allow a large number of samples to be processed in clinical laboratories.

Arnal, C., V. Ferre-Aubineau, et al. (1999). "Comparison of seven RNA extraction methods on stool and shellfish samples prior to hepatitis A virus amplification." J Virol Methods 77(1): 17-26.
	When choosing an extraction method, two parameters have to be considered: recovery of the viral material and elimination or inactivation of inhibitory substances. Seven techniques for extracting hepatitis A virus (HAV) from stool and shellfish samples were compared, in order to identify the protocol most suited to both types of sample and with the best extraction yield. The protocols tested were either techniques for the recovery and purification of total RNA, such as RNAzol, PEG-CETAB, GTC-silica and Chelex, or techniques for isolating specifically HAV using a nucleotide probe or a monoclonal antibody. For stool samples, RNAzol, PEG-CETAB, and magnetic beads with antibody allowed detection of the virus in 11/12 and 12/12 of samples. For shellfish samples, three protocols allowed RNA to be extracted in 90% of cases, RNAzol, PEG-CETAB, and GTC-silica. Their rapidity and low cost make RNAzol and GTC-silica the most suitable for routine diagnostic testing. reserved.

Arnal, C., V. Ferre-Aubineau, et al. (1999). "Quantification of hepatitis A virus in shellfish by competitive reverse transcription-PCR with coextraction of standard RNA." Applied and Environmental Microbiology 65(1): 322-326.
	To quantify hepatitis A virus (HAV) in experimentally contaminated mussels, we developed an internal standard RNA with a 7-nucleotide deletion for competitive reverse transcription (RT)-PCR. Deposited directly into the sample, this standard was used both as extraction control and as quantification tool. After coextraction and competitive RT-PCR, standard and wild-type products were detected by differential hybridization with specific probes and a DNA enzyme immunoassay. The quantifiable range with this reproducible method was 10(4) to 10(7) copies of HAV/gram or 400 to 10(6) 50% tissue culture infective doses/ml. 

Arness, M. F. B. C. M. T. D. M. S. C. T. H. E. P. C. C. J. F. R. H. C. B. T. J. C. S. D. (2000). "Norwalk-like viral gastroenteritis outbreak in U.S. Army trainees." Emerging Infectious Diseases 66(2): 204-7.
	An outbreak of acute gastroenteritis hospitalized 99 (12%) of 835 U. S. Army trainees at Fort Bliss, El Paso, Texas, from August 27 to September 1, 1998. Reverse transcriptase polymerase chain reaction tests for Norwalk-like virus were positive for genogroup 2. Gastroenteritis was associated with one post dining facility and with soft drinks.

Arness, M. K., B. H. Feighner, et al. (2000). "Norwalk-like viral gastroenteritis outbreak in U.S. Army trainees." Emerg Infect Dis 6(2): 204-7.
	An outbreak of acute gastroenteritis hospitalized 99 (12%) of 835 U. S. Army trainees at Fort Bliss, El Paso, Texas, from August 27 to September 1, 1998. Reverse transcriptase polymerase chain reaction tests for Norwalk-like virus were positive for genogroup 2. Gastroenteritis was associated with one post dining facility and with soft drinks.

Arribas, R. M., A. Bosch, et al. (1988). "Survey of Viral Pollution in Duero River Spain Occurrence of Natural Virucidal Phenomena." Environment International 14(1): 37-42.
	A 17-month survey was undertaken to monitor the occurrence of enteroviruses at five sampling stations along the Duero River, in the vicinity of Soria. Total aerobic bacteria, total and faecal coliforms and fecal streptococci, together with several physicochemical parameters were also analysed. Although all the bacterial populations under study correlated to each other, no correlation was demonstrated between virus levels and any other parameter. Virus depuration processes were verified to occur. The river acquires a high level of fecal contamination after the discharge of a heavily contaminated urban sewage outfall. A progressive decrease in virus levels was observed along the river course, showing the effectiveness of natural virus inactivation phenomena occurring in the river.

Asanaka, M., R. L. Atmar, et al. (2005). "Replication and packaging of Norwalk virus RNA in cultured mammalian cells." Proc Natl Acad Sci U S A 102(29): 10327-32.
	Human noroviruses, the most common cause of nonbacterial gastroenteritis, are characterized by high infectivity rate, low infectious dose, and unusually high stability outside the host. However, human norovirus research is hindered by the lack of a cell culture system and a small animal model of infection. Norwalk virus (NV) is the prototype strain of human noroviruses. We report here replication of NV viral RNA and its packaging into virus particles in mammalian cells by intracellular expression of native forms of NV viral RNA devoid of extraneous nucleotide sequences derived from the expression vector by the use of replication-deficient vaccinia virus MVA encoding the bacteriophage T7 RNA polymerase (MVA/T7). Expressed genomic RNA was found to replicate; NV subgenomic RNA was transcribed from genomic RNA by use of NV nonstructural proteins expressed from genomic RNA and was subsequently translated into NV capsid protein VP1. Viral genomic RNA was packaged into virus particles generated in mammalian cells. The cesium chloride (CsCl) density gradient profile of virus particles containing genomic RNA was similar to that of NV purified from stool. These observations indicate that the NV cDNA constructed here is a biologically infectious clone, and that mammalian cells have the ability to replicate NV genomic RNA. This work establishes a mammalian cell-based system for analysis of human norovirus replication and, thus, makes it feasible to investigate antiviral agents in mammalian cells.

Ascione, R. and G. F. Vande Woude (1969). "Inhibition of host cell ribosomal ribonucleic acid methylation by foot-and-mouth disease virus." J Virol 4(5): 727-37.
	
Atmar, R. L. and M. K. Estes (2001). "Diagnosis of noncultivatable gastroenteritis viruses, the human caliciviruses." Clin. Microbiol. Rev. 14(1): 15-37.
	Gastroenteritis is one of the most common illnesses of humans, and many different viruses have been causally associated with this disease. Of those enteric viruses that have been established as etiologic agents of gastroenteritis, only the human caliciviruses cannot be cultivated in vitro. The cloning of Norwalk virus and subsequently of other human caliciviruses has led to the development of several new diagnostic assays. Antigen detection enzyme immunoassays (EIAs) using polyclonal hyperimmune animal sera and antibody detection EIAs using recombinant virus-like particles have supplanted the use of human-derived reagents, but the use of these assays has been restricted to research laboratories. Reverse transcription-PCR assays for the detection of human caliciviruses are more widely available, and these assays have been used to identify virus in clinical specimens as well as in food, water, and other environmental samples. The application of these newer assays has significantly increased the recognition of the importance of human caliciviruses as causes of sporadic and outbreak-associated gastroenteritis.

Atmar, R. L. and M. K. Estes (2006). "The epidemiologic and clinical importance of norovirus infection." Gastroenterol Clin North Am 35(2): 275-90, viii.
	Noroviruses are a major cause of sporadic cases and epidemic outbreaks of gastroenteritis. The development of molecular diagnostic assays has led to an increased recognition of the significance of these viruses as causes of gastroenteritis in all age groups. This article reviews the epidemiology, clinical manifestations and pathogenesis of norovirus infection, and it describes the diagnostic and therapeutic approaches to this disease.

Atmar, R. L., T. G. Metcalf, et al. (1993). "Detection of enteric viruses in oysters by using the polymerase chain reaction." Applied and Environmental Microbiology 59(2): 631-635.
	A procedure for the detection of enteric viral nucleic acid in oysters by the polymerase chain reaction was developed. Known quantities of poliovirus type 1 were seeded into oysters. Virus was extracted and concentrated by using organic flocculation and polyethylene glycol precipitation. Inhibitors of reverse transcription-polymerase chain reaction were present in the oyster extracts, preventing amplification of target viral nucleic acid. The use of cetylrimethylammonium bromide precipitation sufficiently removed inhibitors to allow detection of as few as 10 PFU of poliovirus. Norwalk virus also could be detected after being seeded into oysters. This methodology may be useful for the detection of these and other shellfish-borne viral pathogens.

Atmar, R. L., F. H. Neill, et al. (1995). "Detection of Norwalk virus and hepatitis A virus in shellfish tissues with the PCR." Applied and Environmental Microbiology 61(8): 3014-3018.
	A method for the detection of Norwalk virus and hepatitis A virus from shellfish tissues by PCR was developed. Virus was added to the stomach and hepatopancreatic tissues of oysters or hard-shell clams, and viral nucleic acids were purified by a modification of a previously described method (R.L. Atmar, T.G. Metcalf, F.H. Neill, and M.K. Estes, Appl. Environ. Microbiol. 59:631-635, 1993). The new method had the following advantages compared with the previously described method: (i) more rapid sample processing; (ii) increased test sensitivity; (iii) decreased sample-associated interference with reverse transcription-PCR; and (iv) use of chloroform-butanol in place of the chlorofluorocarbon trichlorotrifluoroethane. In addition, internal standards for both Norwalk virus and hepatitis A virus were made which demonstrated when inhibitors to reverse transcription-PCR were present and allowed quantitation of the viral nucleic acids present in samples. This assay can be used to investigate shellfish-associated gastroenteritis outbreaks and to study factors involved in virus persistence in shellfish. 

Atmar, R. L., F. H. Neill, et al. (1996). "Collaborative evaluation of a method for the detection of Norwalk virus in shellfish tissues by PCR." Applied and Environmental Microbiology 62(1): 254-258.
	A multicenter, collaborative trial was performed to evaluate the reliability and reproducibility of a previously described method for the detection of Norwalk virus in shellfish tissues with the PCR (R.L. Atmar, F. H. Neill, J. L. Romalde, F. Le Guyader, C. M. Woodley, T. G. Metcalf, and M. K. Estes, Appl. Environ. Microbiol. 61:3014-3018, 1995). Virus was added to the stomachs and hepatopancreatic tissues of oysters or hard-shell clams in the control laboratory, the samples were shipped to the participating laboratories, and viral nucleic acids were extracted and then detected by reverse transcription-PCR. The sensitivity and specificity of the assay were 85 and 91%, respectively, when results were determined by visual inspection of ethidium bromide-stained agarose gels; the test sensitivity and specificity improved to 87 and 100%, respectively, after confirmation by hybridization with a digoxigenin-labeled, virus-specific probe. We have demonstrated that this method can be implemented successfully by several laboratories to detect Norwalk virus in shellfish tissues. 

Atoynatan, T. and G. D. Hsiung (1964). "Ultrafiltration of simian viruses." Proc. Soc. Exp. Biol. Med. 116: 852-856.
	
Ausar, S. F., T. R. Foubert, et al. (2006). "Conformational stability and disassembly of Norwalk virus-like particles. Effect of pH and temperature." J Biol Chem 281(28): 19478-88.
	Greater than 99% of the Norwalk virus (NV) capsid consists of 180 copies of a single 58-kDa protein. Recombinantly expressed monomers self-assemble into virus-like particles (VLPs) with a well defined icosahedral structure. NV-VLPs are an appropriate vaccine antigen since the antigenic determinants of the parent virion are preserved. They also constitute very simple models to study the mechanisms of assembly and disassembly of viral capsids. This work examines the inherent stability of NV-VLPs over a range of pH and temperature values and provides detailed insight into structural perturbations that accompany disassembly. The NV-VLP structure was monitored using a variety of biophysical techniques including intrinsic and extrinsic fluorescence, high resolution second-derivative UV absorption spectroscopy, circular dichroism (CD), dynamic light scattering, differential scanning calorimetry, and direct observation employing transmission electron microscopy. The data demonstrate that NV-VLPs are highly stable over a pH range of 3-7 and up to 55 degrees C. At pH 8, however, reversible capsid dissociation was correlated with increased solvent exposure of tyrosine residues and subtle changes in secondary structure. Above 60 degrees C NV-VLPs undergo distinct phase transitions arising from secondary-, tertiary-, and quaternary-level protein structural perturbations. By combining the spectroscopic data employing a multidimensional eigenvector phase space approach, an empirical phase diagram for NV-VLP was constructed. This strategy of visualization provides a comprehensive description of the physical stability of NV-VLP over a broad range of pH and temperature. Complementary, differential scanning calorimetric analyses suggest that the two domains of VP1 unfold independently in a pH-dependent manner.

Avellon, A., P. Perez, et al. (2001). "Rapid and sensitive diagnosis of human adenovirus infections by a generic polymerase chain reaction." J Virol Methods 92(2): 113-20.
	A new adenovirus specific nested polymerase chain reaction (PCR) method is described. It was designed inside the hexon protein gene of the adenovirus genome, and was able to detect DNA of all 47 human adenovirus types in a wide range of clinical samples. A sensitive internal control system able to assure proper analytical conditions for the amplification of as few as 100 molecules of a heterologous DNA was included to avoid false negative results. Sensitivity was estimated at about 10 molecules per tube of a plasmid containing an insert of the first amplification product. The method was able to detect adenovirus infection in 31/43 conjunctival scrapings from patients with acute kerato conjunctivitis 10/40 nasopharyngeal aspirates from patients admitted to hospital with acute respiratory disease and 2/26 urine samples from patients with haemorrhagic cystitis with better sensitivity than cell culture or rapid diagnosis by antigen detection by immunofluorescence (IF) in the case of respiratory specimens. Only two of 17 stools positive for a group F adenovirus specific latex immunoassay were PCR negative. The internal control system avoided a false negative result on another two stool samples. In conclusion, the method described below was shown to be useful for rapid diagnosis of adenovirus infections with higher sensitivity than antigen detection by IF.

Aycock, W. L. (1927). "A milk-borne epidemic of poliomyelitis." Am. J. Hyg. 7: 791-803.
	not available

Aye, T. T., X. M. T. Uchida, et al. (1992). "Sequence comparison of th capsid region of hepatitis E viruses isolated from Myanmar and China." Microbiology and Immunology 36(6): 615-621.
	Hepatitis E viruses (HEVs) were isolated during epidemics, one from Myanmar (formerly called Burma) and one from China and were partially sequenced. Another HEV Myanmar strain from sporadic hepatitis was previously sequenced by us. A cDNA sequence comparison was performed among them in the 3'-terminal region, approximately 750-base long. This region contained at least two immunological epitopes and was considered to correspond to the structural protein. The nucleotide sequence identity was 97.2% between the two Myanmar strains and 93.3 and 92.5% between the two Myanmar and the China strain. The deduced amino acid sequence identity ranged from 98.4 to 100.0% among the three strains. Thus this segment was well conserved on the amino acid level among the different strains isolated from these two Asian countries, although the China strain diverged more from the Myanmar strains on the nucleotide sequence level. This data may provide important information for the development of a vaccine and for identification of the virological link between different geographical locations. 

Azevedo, M. S., L. Yuan, et al. (2005). "Viremia and nasal and rectal shedding of rotavirus in gnotobiotic pigs inoculated with Wa human rotavirus." J Virol 79(9): 5428-36.
	Respiratory symptoms with rotavirus shedding in nasopharyngeal secretions have been reported in children with and without gastrointestinal symptoms (Zheng et al., 1991, J. Med. Virol. 34:29-37). To investigate if attenuated and virulent human rotavirus (HRV) strains cause upper respiratory tract infections or viremia in gnotobiotic pigs, we inoculated them with attenuated or virulent HRV intranasally, intravenously, or orally or via feeding tube (gavage) and assayed virus shedding. After oral or intranasal inoculation with attenuated HRV, the pigs remained asymptomatic, but 79 to 95% shed virus nasally and 5 to 17% shed virus rectally. After inoculation by gavage, no pigs shed virus nasally or rectally, but all pigs seroconverted with antibodies to HRV. No viremia was detected through postinoculation day 10. Controls inoculated intranasally with nonreplicating rotavirus-like particles or mock inoculated did not shed virus. In contrast, 100% of pigs inoculated with virulent HRV (oral, intranasal, or gavage) developed diarrhea, shed virus nasally and rectally, and had viremia. The infectivity of sera from the viremic virulent HRV-inoculated pigs was confirmed by inoculating gnotobiotic pigs orally with pooled HRV-positive serum. Serum-inoculated pigs developed diarrhea and fecal and nasal virus shedding and seroconverted with serum and intestinal HRV antibodies. Pigs inoculated intravenously with serum or intestinal contents from the viremic virulent HRV-inoculated pigs developed diarrhea, virus shedding, and viremia, similar to the orally inoculated pigs. This study provides new evidence that virulent HRV causes transient viremia and upper respiratory tract infection in addition to gastrointestinal infection in gnotobiotic pigs, confirming previous reports of rotavirus antigenemia (Blutt et al., Lancet 362:1445-1449, 2003). Our data also suggest that intestinal infection might be initiated from the basolateral side of the epithelial cells via viremia. Additionally, virus shedding patterns indicate a different pathogenesis for attenuated versus virulent HRV.

Babich, H. and G. Stotzky (1980). "Reductions in Inactivation Rates of Baceriophages by Clay Minerals in Lake Water." Water Research Vol 14: No 2, p 185-187.
	The effect of clay minerals on the survival of bacteriophages of Eschrichia coli and Staphylococcus aureus were studied in natural water samples from the freshwater Lake Kauneonga. Clay preparations of kaolinite, montmorillonite, vermicullite, or attapulgite clays were added at different concentrations to test tubes of lake water inoculated with two phages of E. coli and three of S. aureus. The test tubes were serially diluted with buffer and applied to appropriate host bacterial cultures on agal plates. Plaques were counted after 18 hr of incubation. Results showed variations in the stabilities of bacteriophages in natural lake water. The rate of inactivation of an S. aureus phage was found to be greatly reduced in the presence of clay minerals in either filtered or autoclaved or unautoclaved lake water with the sequence of protection being attapulgite>vermiculite>montmorillonite, kaolinite. The viral protection afforded by the clays was attributed to the adsorption of the viruses onto the clay particles in the lake water suspensions. Lake of protection of viruses by the addition of humic acids or heat-killed microbial cells in other experiments could have been due to the inability of these materials to successfully adsorb the viruses. (Geiger-FRC)

Bachrach, H. L. and G. F. Vande Woude (1968). "Amino acid composition and C-terminal sequence of foot-and-mouth disease virus protein." Virology 34(2): 282-9.
	
Badawy, A. S., C. P. Gerba, et al. (1985). "Survival of rotavirus SA-11 on vegetables." Food Microbiology 2(3): 199-205.
	not available

Baert, L., M. Uyttendaele, et al. (2007). "Evaluation of two viral extraction methods for the detection of human noroviruses in shellfish with conventional and real-time reverse transcriptase PCR." Lett Appl Microbiol 44(1): 106-11.
	AIMS: Comparison of two viral extraction methods in order to establish a sensitive and simple detection method for human noroviruses (NV) in bivalve shellfish. METHODS AND RESULTS: A direct RNA extraction method and an alkaline virus elution-concentration method were tested on artificially contaminated mussels. The latter used an alkaline buffer and polyethylene glycol (PEG) to isolate and concentrate the virus particles from shellfish. In both methods Trizol was used to release RNA. The final RNA extracts were amplified and detected with conventional and real-time reverse transcriptase PCR. The direct RNA extraction method was not able to detect low inoculation levels. However, the virus elution-concentration method was more sensitive. CONCLUSIONS: The alkaline elution-PEG concentration method followed by Trizol effectively removed inhibitory components and fulfilled the demands to be a useful tool for routine testing of shellfish for NV detection. SIGNIFICANCE AND IMPACT OF THE Study: Because of the lack of standardized methods to detect NV in shellfish, many 'in-house' extraction methods are used in practice. A comparison of these methods aims to determine a simple, rapid and sensitive method that could be a candidate method for screening suspected shellfish.

Baert, L., M. Uyttendaele, et al. (2008). "Evaluation of viral extraction methods on a broad range of Ready-To-Eat foods with conventional and real-time RT-PCR for Norovirus GII detection." Int J Food Microbiol 123(1-2): 101-8.
	Noroviruses (NoV) are a common cause of foodborne outbreaks. In spite of that, no standard viral detection method is available for food products. Therefore, three viral elution-concentration methods and one direct RNA isolation method were evaluated on a broad range of Ready-To-Eat (RTE) food products (mixed lettuce, fruit salad, raspberries and two RTE dishes) artificially seeded with a diluted stool sample contaminated with NoV genogroup II. These seeding experiments revealed two categories of RTE products, fruits and vegetables grouped together and RTE dishes (penne and tagliatelle salads) which are rich in proteins and fat formed another category. The RNA extracts were amplified and detected with two conventional RT-PCR systems (Booster and Semi-nested GII) and one real-time RT-PCR (Real-time GII) assay. A fast direct RNA isolation method detected 10(2) RT-PCRU on 10 g penne and tagliatelle salads with the conventional RT-PCR assays. However real-time RT-PCR was less sensitive for penne salad. A viral elution-concentration method, including a buffer solution for the elution step and one polyethylene glycol (PEG) precipitation step, was able to detect 10(2) RT-PCRU on 50 g frozen raspberries with conventional and real-time RT-PCR assays. Moreover the latter extraction method used no environmental hazardous chemical reagents and was easy to perform.

Baert, L., M. Uyttendaele, et al. (2008). "The reduction of murine norovirus 1, B. fragilis HSP40 infecting phage B40-8 and E. coli after a mild thermal pasteurization process of raspberry puree." Food Microbiol 25(7): 871-4.
	Pasteurization processes of raspberry puree are nowadays limited to short times and rather low temperatures to maintain flavor and nutritional quality. Norovirus (NoV) outbreaks associated with raspberries highlight the need to determine the survival of NoV on this type of soft fruit. Therefore, resistance of murine norovirus 1 (MNV-1), a surrogate for human NoV, B. fragilis HSP40 infecting phage B40-8, and E. coli towards mild pasteurization was tested. Raspberry puree heat treated at 65 degrees C for 30s showed a 1.86, 2.77, and 3.89 log reduction of, respectively, MNV-1, E. coli, and B40-8. Heating at 75 degrees C for 15s established a 2.81 log reduction of MNV-1 while a 3.44 and 3.61 log reduction of B40-8 and E. coli was observed. No supplementary lethal effect of holding the heat-treated raspberry puree at 4 degrees C overnight was noticed. B40-8 failed to be useful as a tool to monitor NoV inactivation during mild pasteurization processes. Moreover, <3 log reductions of MNV-1 were observed suggesting that upon high initial contamination load, infectious NoV particles may remain on mildly pasteurized raspberry puree.

Baert, L., M. Uyttendaele, et al. (2008). "Survival and transfer of murine norovirus 1, a surrogate for human noroviruses, during the production process of deep-frozen onions and spinach." J Food Prot 71(8): 1590-7.
	The reduction of murine norovirus 1 (MNV-1) on onions and spinach by washing was investigated as was the risk of contamination during the washing procedure. To decontaminate wash water, the industrial sanitizer peracetic acid (PAA) was added to the water, and the survival of MNV-1 was determined. In contrast to onions, spinach undergoes a heat treatment before freezing. Therefore, the resistance of MNV-1 to blanching of spinach was examined. MNV-1 genomic copies were detected with a real-time reverse transcription PCR assay in PAA-treated water and blanched spinach, and PFUs (representing infectious MNV-1 units) were determined with a plaque assay. A < or = 1-log reduction in MNV-1 PFUs was achieved by washing onion bulbs and spinach leaves. More than 3 log PFU of MNV-1 was transmitted to onion bulbs and spinach leaves when these vegetables were washed in water containing approximately 5 log PFU/ml. No decline of MNV-1 occurred in used industrial spinach wash water after 6 days at room temperature. A concentration of 20 ppm of PAA in demineralized water (pH 4.13) and in potable water (pH 7.70) resulted in reductions of 2.88 +/- 0.25 and 2.41 +/- 0.18 log PFU, respectively, after 5 min of exposure, but no decrease in number of genomic copies was observed. No reduction of MNV-1 PFUs was observed on frozen onions or spinach during storage for 6 months. Blanching spinach (80 degrees C for 1 min) resulted in at least 2.44-log reductions of infectious MNV-1, but many genomic copies were still present.

Baert, L., I. Vandekinderen, et al. (2008). "Inactivation of murine norovirus 1 and Bacteroides fragilis infecting phage B40-8 by the use of sodium hypochlorite and peroxyacetic acid as decontaminating agents for shredded iceberg lettuce." Commun Agric Appl Biol Sci 73(1): 97-101.
	
Baert, L., C. E. Wobus, et al. (2008). "Detection of murine norovirus 1 by using plaque assay, transfection assay, and real-time reverse transcription-PCR before and after heat exposure." Appl Environ Microbiol 74(2): 543-6.
	The correlation between the detection of murine norovirus 1 RNA by real-time reverse transcription-PCR and the infectivity by plaque assay before and after heat exposure (80 degrees C) was examined. No correlation was found in the current study. Moreover, heat inactivation had a much stronger detrimental effect on virus infectivity than on the integrity of the viral genome.

Bagdasaryan, G. A. (1964). "Survival of Viruses of the Enterovirus Group (Poliomyelitis, Echo, Coxsackie) in Soil and on Vegetables." J Hyg Epidemiol Microbiol Immunol 120: 497-505.
	
Baggi, F. and R. Peduzzi (2000). "Genotyping of rotaviruses in environmental water and stool samples in Southern Switzerland by nucleotide sequence analysis of 189 base pairs at the 5' end of the VP7 gene." J Clin Microbiol 38(10): 3681-5.
	Stool specimens from children (<4 years old) with diarrhea were collected over a 1-year period in Ticino (southern region of Switzerland). During the same period, environmental samples were collected from surface waters in the proximity of major water treatment plants. From treatment plants, samples were collected from the raw sewage and before the release of the treated water. From rivers, samples were collected before and after receiving the treated waters. A single-step reverse transcription (RT)-PCR amplification of the entire VP7 gene from extracted double-stranded RNA was developed. For the water samples, a further nested PCR was necessary to increase sensitivity. All amplified viral products were sequenced, and the sequence profile was compared to that of the VP7 genes of human and animal rotaviruses from GenBank. Rotavirus strains are characterized by outer capsid proteins G (glycoprotein) and P (protease-cleaved protein). Correct G genotyping of viral sequences from stool and water samples was possible by analyzing only 189 bp at the 5' end of the VP7 gene. In the Ticino region, the most predominant G genotype among clinical and water samples was G1. Genotypes G2 and G4 were found only among clinical samples. We also detected rotavirus G1-type sequences in feces from a healthy adult. This finding corroborates the hypothesis that healthy adults act as potential reservoirs for the spread of rotavirus in the environment. In our experiments, this RT-PCR-based method for rotavirus genotyping has proven to be a useful tool for epidemiological investigations.

Bajolet, O. and C. Chippaux-Hyppolite (1998). "[Rotavirus and other viruses of diarrhea]." Bull Soc Pathol Exot 91(5 Pt 1-2): 432-7.
	Rotaviruses represent 80% of recognized viral etiologies and 140 million cases of diarrhea per year. They strike young children with similar frequency throughout the world, but the mortality rate is high in developing countries only, with some 870,000 deaths per year (WHO, 1997). Rotaviruses belong to the family of Reoviridae; they are segmented bicatenary RNA viruses, which explains their genetic variability, the presence of mixed infections, the establishment for some time already of a molecular epidemiology by electrophore types. The viruses are "naked" and thus resistant to the outside environment; their massive elimination, 10(8) to 10(10)viral particles per gram of faeces, begins with the first day of diarrhea. They are found in used water and can also be concentrated by shellfish; the environment thus constitutes a notable reservoir for the virus. Oral-faecal transmission is facilitated by deficient sanitary conditions. The 11 fragments of the genome each codify for 1 viral protein; 2 surface proteins, VP4 and VP7, bring about the formation of neutralizing antibodies, which are important for the protection and determination of different serotypes. A non structural protein--NSP4--would seem to intervene in the cytopathogenic effect and may act as a veritable viral enterotoxine. Numerous animal species are infected by rotaviruses which are district from the human ones. The pathology as it affects animals is of economic importance and of interest as an experimental and vaccinal model. Between human and animal rotaviruses there can be genetic rematchings and the VP6 protein is an antigen common to the group. The description of the other viruses responsible for diarrhea has benefited from widespread use of electronic microscopes from the very first years of study of rotaviruses. These other viruses belong to 6 different types: adenovirus, calcivirus, astrovirus, Norwalk agent and related viruses, coronavirus, enterovirus. They therefore have a structural and antigenic polymorphism but, except for the coronavirus, they are all "naked" virions with resistance in outside environments and means of transmission analogous to the rotaviruses. Clinical signs of viral gastroenterites, the age of the patient and epidemiological circumstances help in making an etiological diagnosis; the biological diagnosis has been simplified for the rotaviruses and the adenoviruses. Epidemics related to food, or of hydric and nosocomial origin, especially those due to the Norwalk agent, are under-declared and more frequent than those of bacterial origin. The prevention of dangers related to faeces, the improvement of sanitary conditions, health education, and better nutrition contribute to rotavirus prevention, but rotavirus diarrheas, the incidence of which is similar in developed and developing countries, would be more efficiently controlled through vaccination.

Baker, K. H. (1995). "Detection and occurrence of indicator organisms and pathogens." Water Environment Research 67, no. 4: 406-410.
	This review covers the detection and occurrence of bacterial, protozoan and viral indicator oganisms and pathogens in drinking water and wastewater. In view of the continued emergence of infections carried by water-borne routes, opportunistic pathogens and non-traditional indicators are included also.

Baker, K. H. and J. P. Hegarty (1997). "Detection and occurrence of indicator organisms and pathogens." Water Environment Research: vol. 69, no. 4, pp. 403-415.
	Geldrich (1996) reviewed the detection and occurrence of pathogenic organisms, including bacteria, enteric viruses, protozoa, and parasitic worms, in freshwater supplies. He summarized an enormous amount of data on the sources of these organisms, their occurrence, and their detection in water supplies. Because routine monitoring for pathogens is often unrealistic, Geldrich argued that the use of indicator organisms, specifically coliforms and fecal coliforms, should be the mainstay of routine monitoring programs. He suggested that the lack of correlation between these organisms and pathogens such as protozoa and viruses may be a reflection of the vast difference in sample sizes used for the analysis (100 mL for coliforms versus greater than 1 L for viruses and protozoa) and recommended that the standard sample size for analysis of indicator organisms should be increased. Finally, Geldrich presented several case studies of waterborne disease outbreaks with a complete discussion of not only the source of the pathogenic organisms but also the measures that were successful in controlling the outbreaks. Gale (1996), in a review of microbial risk assessment, also addressed the difficulties in comparing densities of indicator organisms from samples of different volumes. As he noted, current information on the occurrence of pathogens in drinking water supplies is only available for sample volumes significantly larger that the amount ingested daily by any individual, and little information is available on how organisms are dispersed within these large volumes. This makes the estimation of risk to the individual consumer difficult, if not impossible, to determine. Dufour (1996) and Edberg (1996) reviewed water and wastewater microbiology. Both emphasized the importance of enzymatic and molecular techniques in the detection and enumeration of indicator bacteria. Busse et al. (1996) reviewed the techniques available for the identification of bacteria. In addition to the traditional biochemical and physiological tests, they discussed more recent chemotaxonomic approaches such as analysis of quinone system, fatty acid profiles, polar lipid patterns, polyamine patterns, whole cell sugars, and peptidoglycan diamino acids; analytical fingerprinting and cellular protein patterning; and nucleic acid techniques such as 16S rDNA (deoxyribonucleic acid) sequencing, restriction fragment length polymorphism (RFLP), macrorestriction analysis, and random amplified polymorphic DNA (RAPD).

Baker, K. H. and D. S. Herson (1999). "Detection and Occurrence of Indicator Organisms and Pathogens." Water Environment Research(5): 530-551.
	Since 1971, the Centers for Disease Control and Prevention (CDC) and the U.S. Environmental Protection Agency (U.S. EPA) have maintained a surveillance system relating to occurrences and causes of waterborne-disease outbreaks (WBDOs). Levy et al. (1998) summarized data for January 1995 through December 1996 and previously unreported outbreaks in 1994. For the period 1995 to 1996, 13 states reported a total of 22 outbreaks associated with drinking water with a total of 2 567 persons becoming ill. No deaths were reported. The microorganism or chemical that caused the outbreak was identified for 14 of the 22 outbreaks. Giardia lamblia and Shigella sonnei each caused two of the outbreaks; Escherichia coli O157:H7, Plesiomonas shigelloides, and a small round structured virus were implicated for one outbreak each. Eleven of the 22 outbreaks were linked to well water, 8 in noncommunity and 3 in community systems. were associated with chemical contamination of the drinking water; the seventh outbreak was attributed to a small round structured virus.

Baker, T. S., N. H. Olson, et al. (1999). "Adding the third dimension to virus life cycles: three-dimensional reconstruction of icosahedral viruses from cryo-electron micrographs." Microbiol Mol Biol Rev 63(4): 862-922, table of contents.
	Viruses are cellular parasites. The linkage between viral and host functions makes the study of a viral life cycle an important key to cellular functions. A deeper understanding of many aspects of viral life cycles has emerged from coordinated molecular and structural studies carried out with a wide range of viral pathogens. Structural studies of viruses by means of cryo-electron microscopy and three- dimensional image reconstruction methods have grown explosively in the last decade. Here we review the use of cryo-electron microscopy for the determination of the structures of a number of icosahedral viruses. These studies span more than 20 virus families. Representative examples illustrate the use of moderate- to low-resolution (7- to 35-A) structural analyses to illuminate functional aspects of viral life cycles including host recognition, viral attachment, entry, genome release, viral transcription, translation, proassembly, maturation, release, and transmission, as well as mechanisms of host defense. The success of cryo-electron microscopy in combination with three- dimensional image reconstruction for icosahedral viruses provides a firm foundation for future explorations of more-complex viral pathogens, including the vast number that are nonspherical or nonsymmetrical.

Balayan, M. S. (1997). "Epidemiology of hepatitis E virus infection." J Viral Hepat 4(3): 155-65.
	Hepatitis E is an acute, icteric, self-limiting disease, which is spread widely in many tropical and subtropical countries where it occurs both in the form of epidemics of variable magnitude or sporadically. Hepatitis E affects young adults, rather than children, and causes a high mortality rate, particularly in pregnant women. In industrialized countries this disease occurs occasionally as imported sporadic cases. The aetiological cause of hepatitis E is a virus, hepatitis E virus (HEV), which is temporally classified as a member of the Calicivirus family, although its genomic composition is unique. There are experimental data as well as epidemiological observations allowing us to assume that hepatitis E may be a zoonosis as HEV is pathogenic for some domestic and wild animals. Recently, serological assays based on the use of recombinant or synthetic antigens were developed and applied to determine the prevalence of antibody to HEV (anti-HEV) in various epidemic and non-epidemic settings. In suspected hepatitis E cases, anti-HEV seropositivity was detected at an elevated rate but the overall seroprevalence of anti-HEV in normal human populations of endemic areas appeared to be unexpectedly low. A low but constant presence of anti-HEV seropositivity was observed also in non-endemic industrialized countries. In some of these countries, anti-HEV seropositivity was accumulated in groups of patients with various liver and non-liver pathologies and certain groups at risk for blood-borne infections.

Balayan, M. S., R. K. Usmanov, et al. (1990). "Brief report: experimental hepatitis E infection in domestic pigs." J Med Virol 32(1): 58-9.
	
Balayan, M. S., R. K. Usmanov, et al. (1990). "Experimental hepatitis E infection in domestic pigs." Journal of Medical Virology 32(1): 58-59.
	not available

Baldwin, M. A. (2001). "Mass spectrometric analysis of prion proteins." Adv Protein Chem 57: 29-54.
	
Bales, R. C., S. R. Hinkle, et al. (1991). "Bacteriophage adsorption during transport through porous media: Chemical perturbations and reversibility." Environmental Science & Technology 25, no. 12: 2088-2095.
	In a series of seven column experiments, attachment of the bacteriophage PRD-1 and MS-2 to silica beads at pH's 5.0-5.5 was at least partially reversible; however, release of attached phage was slow and breakthrough curves exhibited significant tailing. Rate coefficients for attachment and detachment were on the order of 10 super(-4) and 10 super(-6)-10 super(-4)s super(-1), respectively. Corresponding time scales were hours for attachment and days for detachment. The sticking efficiency ( alpha ) for phage attachment was near 0.01. The rate of phage release was enhanced by raising pH and introducing surface-active chemical species, illustrating the importance of chemical perturbations in promoting biocolloid transport. Hydrophobic effects appear to be important for absorption of even relatively hydrophilic biocolloids.

Ballance, G. A. (1954). "Epidemic of infective hepatitis in an Oxford college." British Medical Journal 1: 1071-1074.
	
Bamber, M., H. C. Thomas, et al. (1983). "Acute type A, B, and non-A, non-B hepatitis in a hospital population in London: clinical and epidemiological features." Gut 24(6): 561-564.
	(Summary) The aetiology of acute viral hepatitis in 172 patients admitted to an infectious diseases hospital in North London was: hepatitis A in 88 (51%), hepatitis B in 58 (34%), Epstein-Barr (EB) virus in four (2%) and non-A, non-B in 22 (13%). NANB hepatitis was a milder disease than that associated with the other viruses. It predominantly occurred in young men (77%). In half of the cases there was evidence of parenteral transmission. It was not transmitted by sexual contact. 

Banks, M., R. Bendall, et al. (2004). "Human and porcine hepatitis E virus strains, United Kingdom." Emerg Infect Dis 10(5): 953-5.
	We describe a case of acquired infection of a strain of hepatitis E virus (HEV) with a 100% amino acid identity to the analogous region in strains of HEV circulating in a United Kingdom pig herd. This case further supports the theory that autochthonous HEV infection in industrialized countries is zoonotic.

Banks, M., G. S. Heath, et al. (2004). "Evidence for the presence of hepatitis E virus in pigs in the United Kingdom." Vet Rec 154(8): 223-7.
	Samples of serum, tissue and faeces from two pig herds in England were examined for hepatitis E virus by reverse-transcriptase PCR (RT-PCR), and a virus strain from each herd was partially sequenced. Eleven of 42 faecal samples and 16 of 21 tissue samples from two pigs were positive for the virus by RT-PCR. Analysis of two unique but closely related nucleotide sequences obtained from the two herds showed that the viruses clustered in genotype III (6) with a human strain of the virus from an autochthonously acquired case of acute hepatitis in the UK. An ELISA based on recombinant open reading frame 2 (ORF-2) was used to detect antibodies to hepatitis E virus in 256 pig sera from the UK; 85.5 per cent of the samples were positive, compared with 58 per cent of similar samples from Swedish pigs and 23.5 per cent of samples from Dutch pigs.

Banyai, K., B. Jiang, et al. (2006). "Prevalence and molecular characterization of human group C rotaviruses in Hungary." J Clin Virol 37(4): 317-22.
	BACKGROUND: Group C rotaviruses are recognized enteric pathogens of humans and animals. Human group C rotaviruses have been associated with sporadic episodes and large outbreaks of gastroenteritis in children and adults but their epidemiology and ecology are still unexplored. OBJECTIVES: To collect epidemiological data on group C rotavirus infections among children with gastroenteritis in Hungary and perform molecular characterization on the identified strains. STUDY DESIGN: Fecal samples were collected during the 2003 surveillance in Baranya County, Hungary. The presence of group C rotavirus RNA was investigated by polyacrylamide gel electrophoresis and by reverse transcription-nested polymerase chain reaction for the VP6 gene. The identified strains were further characterized by sequencing and phylogenetic analysis of the VP7, VP6, VP4, and NSP4 genes. RESULTS: Three of 472 samples (0.6%) tested positive for group C rotavirus. Two samples were selected for molecular analysis. Strains BaC 6104/03 and BaC 11549/03 displayed an overall identity of >99.8% and 99.3% at the nucleotide and amino acid level, respectively. The VP7 of the strain BaC 6104/03 was most closely related (99.5% aa) to the Nigerian strain Jajeri, while the VP4s of strains BaC 6104/03 and BaC 11549/03 were more similar (98.1% aa) to strains Belem and 208, detected in Brazil and China, respectively. CONCLUSIONS: Based on this 1-year study, we conclude that group C rotaviruses are not of epidemiological relevance in the etiology of childhood acute gastroenteritis in Hungary. The low sequence divergence between the Hungarian strains suggested that a single group C rotavirus strain circulated in this period in the study area.

Barardi, C. R. M., K. R. Emslie, et al. (1998). "Development of a rapid and sensitive quantitative assay for rotavirus based on flow cytometry." Journal of Virological Methods 74(1): 31-38.
	A very sensitive and accurate Bow cytometry (FC) based method have developed to quantitate rotavirus infection in MA104 cells. Confluent cell monolayers were infected with serial dilutions of rotavirus SA11. After infection. the cells were recovered with the aid of trypsin and then reacted with monoclonal antibody M60 (specific for the rotavirus outer capsid protein, VP7), followed by a second antibody (anti-mouse IgG-FITC). A FACScan FC was used to estimate the number of infected cells, as well as the level of infection. Viral infection was optimised by varying the concentration of trypsin used in the maintenance medium. The FC method enables many cells to be screened quickly for infectivity, and can detect low levels of virus. This method can be adapted to monitor the presence of other viruses in clinical and environmental samples without the need for prolonged periods of adaptation to growth in tissue culture. 

Barardi, C. R. M., H. Yip, et al. (1999). "Flow cytometry and RT-PCR for rotavirus detection in artificially seeded oyster meat." International Journal of Food Microbiology 49(1-2): 9-18.
	A flow cytometry (FC)-based method was developed for the detection of rotavirus in oyster meat using simian rotavirus SA11 as a model. To study virus recovery, oyster meat was injected with rotavirus and the oyster extract used to infect MA104 cell monolayers. Following varying periods of infection, the cells were recovered and reacted with the monoclonal antibody M60 which is specific for the rotavirus group A serotypes 1-4 outer capsid protein, VP7, followed by a second antibody (anti mouse IgG-FITC). A FACScan FC was used to estimate the number of infected cells as well as the level of infection. To evaluate the sensitivity of the method, non-inoculated oysters were processed following the same extraction protocol and, at the end, they were seeded with the same amount of virus used for oyster inoculation. This seeded oyster extract was then used to infect MA104 cells and the number of infected cells determined using the same FC procedure. A semi-nested two-step PCR for detection of rotavirus nucleic acid was undertaken to compare the sensitivity of FC with RT-PCR. Using FC, as little as 0.02 flow cytometry units (fcu) (number of infected cells counted by FC) could be detected after 72 h of cell infection. This is a very similar limit of sensitivity to that obtained with RT-PCR. Both methods are approximately 100 times more sensitive than the plaque-forming units (pfu) assay. 

Bardell, D. (1995). "Herpes simplex virus type 1 applied experimentally to gloves used for food preparation." Journal of Food Protection 58(10): 1150-1152.
	Droplets of saliva containing herpes simplex virus type 1 were placed on latex disposable gloves. The temperature at the surface of the gloved hand was 34 degrees C. There was no loss of infectious virus before 15 min. Between 15 and 30 min there was a 2-log-cycle drop in titer, and infectious virus could still be recovered after 1 h, the longest period tested. The drop in titer was due to drying of the saliva, which occurred at approximately 21 min. Infectious virus was transferred by touch to lettuce and ham at 0 min when the virus-containing droplets were in a liquid condition, and after 30 and 60 min when the droplets were dry.

Bardell, D. (1997). "Survival of herpes simplex virus type 1 on some common foods routinely touched before consumption." Journal of Food Protection 60(10): 1259-1261.
	Droplets of saliva containing herpes simplex virus type 1 were placed on the skin of tomatoes and the upper surface of lettuce leaves. There was no loss of virus infectivity titer at refrigerator temperature (2 degrees C) at any time examined up to 1 h, the longest period tested. At room temperature (22 to 24 degrees C) there was a 2-log drop in titer between 30 and 60 min, but some infectious virus was still present at 1 h. The virus-containing saliva remained in a liquid state at 2 degrees C. At 22 to 24 degrees C the droplets became dry at approximately 50 min. Implications of the findings are discussed.

Barker, J., D. Stevens, et al. (2001). "Spread and prevention of some common viral infections in community facilities and domestic homes." J Appl Microbiol 91(1): 7-21.
	
Barlough, J. E., E. S. Berry, et al. (1987). "Antibodies to marine caliciviruses in the Steller sea lion (Eumetopias jubatus Schreber)." J Wildl Dis 23(1): 34-44.
	Sera from 145 Steller sea lions (76 adults, three subadults, 37 pups, and 29 fetuses) were tested for neutralizing antibodies to nine marine calicivirus serotypes. Antibodies were found to San Miguel sea lion virus (SMSV) types 1, 5, 6, 7, 8, 10 and 13, and to Tillamook (bovine) calicivirus, but no antibodies were found to the walrus calicivirus. Titers (microtiter neutralization assay) ranged from 1:20 to 1:320, with many positive reactions at the higher dilutions (greater than or equal to 1:80). Antibodies to SMSV's 5 and 10 were most common among animals sampled in Alaskan waters, while antibodies to SMSV-6 were most common among pups from the southern Oregon coast. These data provide evidence that Steller sea lions, like their California sea lion (Zalophus c. californianus Lesson) counterparts, have experienced widespread exposure to multiple serotypes of marine caliciviruses.

Barlough, J. E., E. S. Berry, et al. (1987). "Prevalence and distribution of serum neutralizing antibodies to Tillamook (bovine) calicivirus in selected populations of marine mammals." J Wildl Dis 23(1): 45-51.
	Neutralizing antibodies to Tillamook calicivirus (TCV) were found in sera collected from California sea lions (Zalophus c. californianus Lesson) in 1983 and 1984 and in sera collected from Steller sea lions (Eumetopias jubatus Schreber) in 1976 and 1985. The combined prevalence of antibodies for these two species was 10/228 = 4.38%. Titers ranged from 1:20 (five animals), to 1:40 (four animals), to 1:80 (one animal) by standard microtiter neutralization assay. The seropositive pinnipeds were dispersed widely along the margins of the eastern Pacific rim, from the Bering Sea to the Santa Barbara Channel. Antibodies to TCV were not found in sera collected from northern fur seals (Callorhinus ursinus L.), Pacific walruses (Odobenus rosmarus divergens Illiger), seals of the family Phocidae, or several cetacean species. Tillamook calicivirus was isolated originally in 1981 from dairy calves in Oregon; the finding of neutralizing antibodies in two widely distributed species of sea lions suggests the possibility of a marine origin for this agent.

Barlow, K. L., J. Green, et al. (2000). "Viral genome characterisation by the heteroduplex mobility and heteroduplex tracking assays." Rev Med Virol 10(5): 321-35.
	The heteroduplex mobility assay (HMA) is a means of comparing two PCR amplicons or, in the variation known as the heteroduplex tracking assay (HTA), a means of estimating the quasispecies diversity of a viral genome. Heteroduplex assays have many applications including subtyping viral genomes, screening for low frequency variants in a population, scanning the relative genetic diversity across a genome and screening for recombinant clones. They can be used to detect dual infections, superinfections, contaminated blood products and laboratory contaminations. PCR amplicons of about 65% sequence similarity or greater will form heteroduplexes under appropriate conditions, and phylogenetic trees can be drawn from heteroduplex mobility data. While homoduplexes indicate more than 98% similarity between two DNA sequences, heteroduplexes indicate at least seven mismatches in a 500-bp amplicon, or a three-base pair gap in 1000-bp. Minority variants comprising 1% to 5% of the genome population can be detected and quantified by HTA. Thus far, heteroduplex assays have been described for HIV and other lentiviruses, hepatitis C and G viruses, Norwalk-like viruses, influenza, measles and poliovirus. They could be applied to a wide range of other viral species.

Baron, R. C., F. D. Murphy, et al. (1982). "Norwalk gastrointestinal illness: an outbreak associated with swimming in a recreational lake and secondary person-to-person transmission." Am J Epidemiol 115(2): 163-72.
	An outbreak of gastrointestinal illness in which headache, low grade fever and myalgia were common symptoms occurred among persons who visited a recreational park in Macomb County, Michigan, on July 13-16, 1979. The temporal clustering of onsets of 121 persons who were the first in their households to become ill suggested an incubation period ranging from 4-77 hours. A history of swimming in the park's lake was elicited with significantly greater frequency from these persons than from park visitors who were not ill (age standardized odds ratio = 4.8; 95% confidence interval, 1.8-12.7). One hundred twenty-six park visitors who became ill were household contacts of index patients who had swum in the lake; at least 62 of these 126 cases were probably due to secondary transmission. A secondary attack rate of 19% was observed in household contacts who had not visited the park. Serologic studies identified Norwalk virus as the etiologic agent. The source of the contamination of the lake could not be determined. Although some water samples collected just before and after the epidemic period had high coliform counts, the geometric mean coliform density of all samples collected on those days was within the limits established by the Environmental Protection Agency as acceptable for recreational contact water.

Barreiros, M. A., A. A. Alfieri, et al. (2003). "An outbreak of diarrhoea in one-week-old piglets caused by group A rotavirus genotypes P[7],G3 and P[7],G5." Vet Res Commun 27(6): 505-12.
	Thirty-two group A isolates of rotavirus detected in faecal samples from diarrhoeic piglets, were selected for P and G genotyping using a Multiplex RT-PCR. Ten isolates, from animals less than 8 days old, characterized an outbreak of diarrhoea caused by group A rotavirus in animals. P[7],G3 (CRW8-like) and P[7],G5 (OSU-like) genotypes were detected in 5 animals each. Isolates of a group A rotavirus of genotypes compatible with the OSU prototype were those most frequently identified in single infections in older animals (20/32 strains). In addition to these, 20 isolates from piglets with diarrhoea caused by group A rotavirus, collected between May 1998 and June 1999, but not from the outbreak month, were analysed. These isolates were used to compare the types observed on the farm outside the outbreak in May 1999 and the CRW8-like genotype was found in none of these faecal samples. P[7],G5 was the most frequent genotype (10/20 strains). No outbreak of diarrhoea caused by rotavirus in 1-week-old piglets was found in any other period during the 13 months of this study.

Barron, R. D. (1954). "Infectious hepatitis in Army installation in the Kingston area " Canadian Journal of Public Health 43: 25-30.
	
Barton, D. J., E. P. Black, et al. (1995). "Complete replication of poliovirus in vitro: preinitiation RNA replication complexes require soluble cellular factors for the synthesis of VPg-linked RNA." J Virol 69(9): 5516-27.
	Translation of poliovirion RNA in HeLa S10 extracts resulted in the formation of RNA replication complexes which catalyzed the asymmetric replication of poliovirus RNA. Synthesis of poliovirus RNA was detected in unfractionated HeLa S10 translation reactions and in RNA replication complexes isolated from HeLa S10 translation reactions by pulse-labeling with [32P]CTP. The RNA replication complexes formed in vitro contained replicative-intermediate RNA and were enriched in viral protein 3CD and the membrane-associated viral proteins 2C, 2BC, and 3AB. Genome-length poliovirus RNA covalently linked to VPg was synthesized in large amounts by the replication complexes. RNA replication was highly asymmetric, with predominantly positive-polarity RNA products. Both anti-VPg antibody and guanidine HCl inhibited RNA replication and virus formation in the HeLa S10 translation reactions without affecting viral protein synthesis. The inhibition of RNA synthesis by guanidine was reversible. The reversible nature of guanidine inhibition was used to demonstrate the formation of preinitiation RNA replication complexes in reaction mixes containing 2 mM guanidine HCl. Preinitiation complexes sedimented upon centrifugation at 15,000 x g and initiated RNA replication upon their resuspension in reaction mixes lacking guanidine. Initiation of RNA synthesis by preinitiation complexes did not require active protein synthesis or the addition of soluble viral proteins. Initiation of RNA synthesis by preinitiation complexes, however, was absolutely dependent on soluble HeLa cytoplasmic factors. Preinitiation complexes also catalyzed the formation of infectious virus in reaction mixes containing exogenously added capsid proteins. The titer of infectious virus produced in such trans-encapsidation reactions reached 4 x 10(7) PFU/ml. The HeLa S10 translation-RNA replication reactions represent an efficient in vitro system for authentic poliovirus replication, including protein synthesis, polyprotein processing, RNA replication, and virus assembly.

Barton, D. J. and J. B. Flanegan (1993). "Coupled translation and replication of poliovirus RNA in vitro: synthesis of functional 3D polymerase and infectious virus." J Virol 67(2): 822-31.
	Poliovirus RNA polymerase and infectious virus particles were synthesized by translation of virion RNA in vitro in HeLa S10 extracts. The in vitro translation reactions were optimized for the synthesis of the viral proteins found in infected cells and in particular the synthesis of the viral polymerase 3Dpol. There was a linear increase in the amount of labeled protein synthesized during the first 6 h of the reaction. The appearance of 3Dpol in the translation products was delayed because of the additional time required for the proteolytic processing of precursor proteins. 3Dpol was first observed at 1 h in polyacrylamide gels, with significant amounts being detected at 6 h and later. Initial attempts to assay for polymerase activity directly in the translation reaction were not successful. Polymerase activity, however, was easily detected by adding a small amount (3 microliters) of translation products to a standard polymerase assay containing poliovirion RNA. Full-length minus-strand RNA was synthesized in the presence of an oligo(U) primer. In the absence of oligo(U), product RNA about twice the size of virion RNA was synthesized in these reactions. RNA stability studies and plaque assays indicated that a significant fraction of the input virion RNA in the translation reactions was very stable and remained intact for 20 h or more. Plaque assays indicated that infectious virus was synthesized in the in vitro translation reactions. Under optimal conditions, the titer of infectious virus produced in the in vitro translation reactions was greater than 100,000 PFU/ml. Virus was first detected at 6 h and increased to maximum levels by 12 h. Overall, the kinetics of poliovirus replication (protein synthesis, polymerase activity, and virus production) observed in the HeLa S10-initiation factor in vitro translation reactions were similar to those observed in infected cells.

Barton, D. J. and J. B. Flanegan (1997). "Synchronous replication of poliovirus RNA: initiation of negative-strand RNA synthesis requires the guanidine-inhibited activity of protein 2C." J Virol 71(11): 8482-9.
	We report that protein 2C, the putative nucleoside triphosphatase/helicase protein of poliovirus, is required for the initiation of negative-strand RNA synthesis. Preinitiation RNA replication complexes formed upon the translation of poliovirion RNA in HeLa S10 extracts containing 2 mM guanidine HCI, a reversible inhibitor of viral protein 2C. Upon incubation in reactions lacking guanidine, preinitiation RNA replication complexes synchronously initiated and elongated negative-strand RNA molecules, followed by the synchronous initiation and elongation of positive-strand RNA molecules. The immediate and exclusive synthesis of negative-strand RNA upon the removal of guanidine demonstrates that guanidine specifically blocks the initiation of negative-strand RNA synthesis. Readdition of guanidine HCl to reactions synchronously elongating nascent negative-strand RNA molecules did not prevent their continued elongation and completion. In fact, readdition of guanidine HCl to reactions containing preinitiation complexes elongating nascent negative-strand RNA molecules had no effect on subsequent positive-strand RNA synthesis initiation or elongation. Thus, the guanidine-inhibited function of viral protein 2C was not required for the elongation of negative-strand RNA molecules, the initiation of positive-strand RNA molecules, or the elongation of positive-strand RNA molecules. The guanidine-inhibited function of viral protein 2C is required only immediately before or during the initiation of negative-strand RNA synthesis. We suggest that guanidine may block an irreversible structural maturation of protein 2C and/or RNA replication complexes necessary for the initiation of RNA replication.

Barton, D. J., B. J. Morasco, et al. (1999). "Translating ribosomes inhibit poliovirus negative-strand RNA synthesis." J Virol 73(12): 10104-12.
	Poliovirus has a single-stranded RNA genome of positive polarity that serves two essential functions at the start of the viral replication cycle in infected cells. First, it is translated to synthesize viral proteins and, second, it is copied by the viral polymerase to synthesize negative-strand RNA. We investigated these two reactions by using HeLa S10 in vitro translation-RNA replication reactions. Preinitiation RNA replication complexes were isolated from these reactions and then used to measure the sequential synthesis of negative- and positive-strand RNAs in the presence of different protein synthesis inhibitors. Puromycin was found to stimulate RNA replication overall. In contrast, RNA replication was inhibited by diphtheria toxin, cycloheximide, anisomycin, and ricin A chain. Dose-response experiments showed that precisely the same concentration of a specific drug was required to inhibit protein synthesis and to either stimulate or inhibit RNA replication. This suggested that the ability of these drugs to affect RNA replication was linked to their ability to alter the normal clearance of translating ribosomes from the input viral RNA. Consistent with this idea was the finding that the protein synthesis inhibitors had no measurable effect on positive-strand synthesis in normal RNA replication complexes. In marked contrast, negative-strand synthesis was stimulated by puromycin and was inhibited by cycloheximide. Puromycin causes polypeptide chain termination and induces the dissociation of polyribosomes from mRNA. Cycloheximide and other inhibitors of polypeptide chain elongation "freeze" ribosomes on mRNA and prevent the normal clearance of ribosomes from viral RNA templates. Therefore, it appears that the poliovirus polymerase was not able to dislodge translating ribosomes from viral RNA templates and mediate the switch from translation to negative-strand synthesis. Instead, the initiation of negative-strand synthesis appears to be coordinately regulated with the natural clearance of translating ribosomes to avoid the dilemma of ribosome-polymerase collisions.

Barwick, R. S., D. A. Levy, et al. (2000). "Surveillance for waterborne-disease outbreaks--United States, 1997-1998." MMWR CDC Surveill Summ 49(4): 1-21.
	PROBLEM/CONDITION: Since 1971, CDC and the U.S. Environmental Protection Agency (EPA) have maintained a collaborative surveillance system for collecting and periodically reporting data relating to occurrences and causes of waterborne-disease outbreaks (WBDOs). REPORTING PERIOD COVERED: This summary includes data from January 1997 through December 1998 and a previously unreported outbreak in 1996. DESCRIPTION OF THE SYSTEM: The surveillance system includes data regarding outbreaks associated with drinking water and recreational water. State, territorial, and local public health departments are primarily responsible for detecting and investigating WBDOs and voluntarily reporting them to CDC on a standard form. RESULTS: During 1997-1998, a total of 13 states reported 17 outbreaks associated with drinking water. These outbreaks caused an estimated 2,038 persons to become ill. No deaths were reported. The microbe or chemical that caused the outbreak was identified for 12 (70.6%) of the 17 outbreaks; 15 (88.2%) were linked to groundwater sources. Thirty-two outbreaks from 18 states were attributed to recreational water exposure and affected an estimated 2,128 persons. Eighteen (56.3%) of the 32 were outbreaks of gastroenteritis, and 4 (12.5%) were single cases of primary amebic meningoencephalitis caused by Naegleria fowleri, all of which were fatal. The etiologic agent was identified for 29 (90.6%) of the 32 outbreaks, with one death associated with an Escherichia coli O157:H7 outbreak. Ten (55.6%) of the 18 gastroenteritis outbreaks were associated with treated pools or ornamental fountains. Of the eight outbreaks of dermatitis, seven (87.5%) were associated with hot tubs, pools, or springs. INTERPRETATION: Drinking water outbreaks associated with surface water decreased from 31.8% during 1995-1996 to 11.8% during 1997-1998. This reduction could be caused by efforts by the drinking water industry (e.g., Partnership for Safe Water), efforts by public health officials to improve drinking water quality, and improved water treatment after the implementation of EPA's Surface Water Treatment Rule. In contrast, the proportion of outbreaks associated with systems supplied by a groundwater source increased from 59.1% (i.e., 13) during 1995-1996 to 88.2% (i.e., 15) during 1997-1998. Outbreaks caused by parasites increased for both drinking and recreational water. All outbreaks of gastroenteritis attributed to parasites in recreational water were caused by Cryptosporidium, 90% occurred in treated water venues (e.g., swimming pools and decorative fountains), and fecal accidents were usually suspected. The data in this surveillance summary probably underestimate the true incidence of WBDOs because not all WBDOs are recognized, investigated, and reported to CDC or EPA. ACTIONS TAKEN: To estimate the national prevalence of waterborne disease associated with drinking water, CDC and EPA are conducting a series of epidemiologic studies to better quantify the level of waterborne disease associated with drinking water in nonoutbreak conditions. The Information Collection Rule implemented by EPA in collaboration with the drinking water industry helped quantifythe level of pathogens in surface water. Efforts by CDC to address recreational water outbreaks have included meetings with the recreational water industry, focus groups to educate parents on prevention of waterborne disease transmission in recreational water settings, and publications with guidelines for parents and pool operators.

Bass, D. M., M. Baylor, et al. (1992). "Molecular basis of age-dependent gastric inactivation of rhesus rotavirus in the mouse " Journal of Clinical Investigation 89(6): 1741-1745.
	Rotavirus requires specific proteolytic activation by trypsin for efficient replication in tissue culture. To observe the nature of intestinal proteolytic activation of rotavirus in vivo, metabolically labeled rhesus rotavirus (RRV) grown in the presence of trypsin inhibitors was administered to adult and 10-d-old suckling mice by gavage. In the adult stomach, vp4 was cleaved in a manner distinct from in vitro trypsin cleavage. In the suckling stomach, RRV vp4 remains largely uncleaved. The alternative cleavage in the adult stomach was associated with a profound decrease in viral infectivity. vp4 from RRV recovered from the suckling small intestinal lumen was cleaved in a pattern similar or identical to in vitro trypsin-activated virus with bands comigrating with vp5* and vp8*. In contrast, vp4 was not observed in any recognizable form in RRV recovered from adult intestines. Comparison of infectivity of virus recovered from suckling and adult intestines revealed a 10,000-fold decrease in titer in the virus recovered from the adult intestine. In vitro digestions of RRV revealed that pepsin digestion can cleave RRV vp4 and markedly enhance acid-induced loss of rotavirus infectivity. Subsequent digestion with chymotrypsin removes most of the pepsin cleavage products of vp4. Virus injected directly into jejunal loops of adult mice and virus administered orally to adult mice pretreated with antiacid drugs retained infectivity. These studies indicate the development of gastric acid and pepsin secretion may be an important host defense factor in rotavirus gastroenteritis. 

Battigelli, D. A., M. D. Sobsey, et al. (1993). "The inactivation of hepatitis A virus and other model viruses by UV irradiation." Water Science and Technology 27(3-4): 339-342.
	 The sensitivity of HAV strain HM-175, coxsackievirus type B-5, rotavirus strain SA-11, and bacteriophages MS2 and ØX174 to ultraviolet radiation of 254 nm wavelength in phosphate buffered water was determined. Purified stocks of the viruses were combined and exposed to collimated UV irradiation in a stirred reactor for a total dose of up to 40 mW sec/cm2. Virus survival kinetics were determined from samples removed at dose intervals. The 4 log (99.99%) inactivation doeses for HAV, CB5, SA-11 and ØX174 were 16, 29, 42, and 9 mW sec/cm2, respectively. MS2 exhibited the greatest resistance in buffered water with less than 1 log reduction observed after exposure to 25 mW sec/cm2. A 15 mW sec/cm2 exposure induced a 7 log reduction of ØX174, while inactivation of HAV, CB5 and SA11 was intermediate, with at least 3 log reductions occurring after a 20 mW sec/cm2 exposure. The results of these experiments indicate that UV irradiation can effectively inactivate viruses of public health concern in drinking water.

Bayas, J. M., A. Gonzalez, et al. (2001). "Cost analysis of two strategies for preventing hepatitis A virus infection in Spanish travellers to developing countries." Epidemiol Infect 127(2): 347-51.
	Our objectives were to assess the prevalence of anti-hepatitis A (HAV) antibodies in Spanish travellers to developing countries and to carry out a cost analysis to allow the comparison of two vaccination strategies. Adult subjects were selected from among travellers to developing countries. Information was obtained on age, sex, destination, previous vaccination against HAV and having received immunoglobulin. Blood specimens were obtained for anti-HAV antibody determination. A total of 485 travellers were studied. The prevalence of anti-HAV antibody was 30.5% (95% CI 26-35). Antibody prevalence was inversely correlated with age: 9.8% in 18-25 years of age, rising to 75.4% in those 41-55 years of age. Cost analysis determined that the critical value of prevalence for vaccination with HAV vaccine was 37.5%. It was concluded that the youngest Spanish travellers lack anti-HAV antibodies. Vaccination without screening in those < or = 35 years of age and screening before vaccination for those > 35 years, are the preferred alternatives.

Bean, N. H., J. S. Goulding, et al. (1996). "Surveillance for foodborne-disease outbreaks--United States, 1988-1992." Morbidity and Mortality Weekly Report 45(5): 1-66.
	PROBLEM/CONDITION: Since 1973, CDC has maintained a collaborative surveillance program for collection and periodic reporting of data concerning the occurrence and causes of foodborne-disease outbreaks (FBDOs). REPORTING PERIOD COVERED: This summary reviews data from January 1988 through December 1992. DESCRIPTION OF SYSTEM: The surveillance system reviews data concerning FBDOs--defined as the occurrence of two or more cases of a similar illness resulting from the ingestion of a common food. Before 1992, only one case of intoxication by chemical, marine toxin, or Clostridium botulinum toxin as a result of the ingestion of food was required to constitute an FBDO. Since 1992, two or more cases have been required. State and local public health departments have primary responsibility for the identifying and investigating FBDOs. State and territorial health departments report these outbreaks to CDC on a standard form. RESULTS: During 1988-1992, a total of 2,423 outbreaks of foodborne disease were reported (451 in 1988, 505 in 1989, 532 in 1990, 528 in 1991, and 407 in 1992). These outbreaks caused a reported 77,373 persons to become ill. Among outbreaks for which the etiology was determined, bacterial pathogens caused the largest percentage of outbreaks (79%) and the largest percentage of cases (90%). Salmonella serotype Enteritidis accounted for the largest number of outbreaks, cases, and deaths; most of these outbreaks were attributed to eating undercooked, infected eggs. Chemical agents caused 14% of outbreaks and 2% of cases; parasites, 2% of outbreaks and 1% of cases; and viruses, 4% of outbreaks and 6% of cases. INTERPRETATION: The number of FBDOs reported per year did not change substantially during the first 4 years but declined in 1992 as a result of the revised definition of an outbreak. During this reporting period, S. Enteritidis continued to be a major cause of morbidity and mortality. In addition, multistate outbreaks caused by contaminated produce and outbreaks caused by Escherichia coli O157:H7 became more prominent. ACTIONS TAKEN: State and local public health departments investigate FBDOs. At the regional and national level, surveillance data provide an indication of the etiologic agents, vehicles of transmission, and contributing factors associated with FBDOs and help direct public health actions. 

Bean, N. H. and P. M. Griffin (1990). "Foodborne disease outbreaks in the United States, 1973-1987: pathogens, vehicles, and trends." Journal of Food Protection 53(9): 804-817.
	The etiologic agents and food vehicles associated with the 7458 outbreaks (involving 237,545 cases) of foodborne disease reported to the Centers for Disease Control between 1973 and 1987 were examined. Bacterial pathogens accounted for 66% of outbreaks and 87% of cases, viruses 5 and 9%, parasites 5 and less than 1%, and chemicals 25 and 4%, respectively. Salmonella accounted for 42% of outbreaks and 51% of cases due to bacterial pathogens. When data from 1973-75 were compared with 1985-87, a 75% increase in the proportion of outbreaks and 130% increase in the proportion of cases due to Salmonella were observed; in particular, outbreaks due to Salmonella enteritidis increased markedly. The proportion of Salmonella outbreaks with a known vehicle that were associated with beef (the food most frequently associated with Salmonella outbreaks) peaked at 30% in 1981, dropped to 4% in 1982, and has since risen gradually. The proportion of Salmonella outbreaks due to chicken and eggs increased over the study period. Bacteria not previously recognized as important foodborne pathogens that emerged during the study period include Campylobacter jejuni, Escherichia coli 0157:H7, and Listeria monocytogenes. Bacterial pathogens accounted for 90% of deaths, with L. monocytogenes (317/1,000 cases) and Clostridium botulinum (192/1,000 cases) having the highest death-to-case ratios. The proportion of outbreaks in which the food was prepared in a commercial or institutional establishment and the median outbreak size both increased. Investigation and analysis of foodborne disease outbreaks continue to play a key role in understanding foodborne illness and in designing and evaluating control measures.

Bean, N. H., P. M. Griffin, et al. (1990). "Foodborne disease outbreaks, 5-year summary, 1983-1987." Morbidity and Mortality Weekly Report 39(1): 15-57.
	This report summarizes data from foodborne disease outbreaks reported to CDC from 1983 through 1987. With a few exceptions, an outbreak is defined as an incident in which two or more persons experience a similar illness and food is implicated. During this period, 2,397 outbreaks of foodborne disease were reported, representing 91,678 cases. Among outbreaks in which the etiology was determined, bacterial pathogens caused the largest number of outbreaks (66%) and cases (92%). Chemical agents caused 26% of outbreaks and 2% of cases. Parasites caused 4% of outbreaks and less than 1% of cases, and viruses caused 5% of outbreaks and 5% of cases. The discrepancies between the number of outbreaks and the number of cases attributed to each etiologic agent emphasizes the importance of evaluating both numbers before drawing conclusions. The etiologic agent was not determined in 62% of outbreaks, reflecting the need for improved investigative skills. The number of outbreaks reported by this surveillance system is only a small fraction of the true number that occur. The likelihood of an outbreak's being reported depends on many factors, such as ease of recognition and ease of laboratory confirmation. Sporadic foodborne illness is far more common and is not included in this report. 

Beards, G. M., A. D. Campbell, et al. (1984). "Enzyme-linked immunosorbent assays based on polyclonal and monoclonal antibodies for rotavirus detection." Journal of Clinical Microbiology 19(2): 248-254.
	We describe two enzyme-linked immunosorbent assays for rotavirus antigen in feces, which were designed to be as sensitive and specific as possible, and easy to use anywhere. Both are indirect methods, using the antibody capture method, but the second assay utilizes a rotavirus group-specific monoclonal "detecting" antibody instead of the hyperimmune polyvalent guinea pig antisera used in the first assay. Both tests were found to be more sensitive than electron microscopy for detecting virus. To develop these tests, solid phase, antiserum production methods, treatment of the test antigen with EDTA, substrate, stability of reagents, and the need for confirmatory "blocking" tests were all examined. The first assay described is that used at present by the World Health Organization for their worldwide diarrheal disease control program.

Beaulieux, F., D. M. See, et al. (1997). "Use of magnetic beads versus guanidium thiocyanate-phenol-chloroform RNA extraction followed by polymerase chain reaction for the rapid, sensitive detection of enterovirus RNA." Research in Virology 148(1): 11-15.
	The current study compares the sensitivity of RNA extraction using magnetic beads versus that of a standard extraction method. Streptavadin-coated magnetic beads were labelled with a biotinylated, enterovirus-specific oligonucleotide. RNA was extracted using labelled beads or guanidium thiocyanate-phenol-chloroform from 1, 0.1 and 0.01 TCID50/100 microliters of stock coxsackievirus types A9 and B3, echovirus type 11, enterovirus type 70 and poliovirus type 1. Each strain was tested three times. RNA extraction using magnetic beads was > 50% faster than the standard method. The RNA was amplified using RT-PCR, and the products were detected using agarose gel electrophoresis; 6/15 and 7/15 samples at an initial concentration of 0.01 TCID50/100 microliters were detected using magnetic beads or standard extraction, respectively. Negative-stain electron microscopy was used to determine that 0.01 TCID50/100 microliters of coxsackievirus B3 contained approximately 3 genomes. Thus, use of magnetic beads labelled with an enterovirus-specific oligonucleotide was less toxic, more rapid and as sensitive as the current standard RNA extraction method.

Beck, E., R. Sommer, et al. (1978). "Nucleotide sequence of bacteriophage fd DNA." Nucleic Acids Res 5(12): 4495-503.
	The sequence of the 6,408 nucleotides of bacteriophage fd DNA has been determined. This allows to deduce the exact organisation of the filamentous phage genome and provides easy access to DNA segments of known structure and function.

Beck, E. and B. Zink (1981). "Nucleotide sequence and genome organisation of filamentous bacteriophages fl and fd." Gene 16(1-3): 35-58.
	The DNA sequence of the filamentous phage F1, consisting of 6407 nucleotides, has been determined. When compared with the DNA sequence of the related filamentous phage fd (Beck et al., 1978), the f1 sequence is one nucleotide shorter and differs in 180 positions from the fd DNA. Only ten of these base exchanges cause amino acid exchanges in the known gene products. Most of the exchanges in f1 are the same as in M13 (Van Wezenbeek et al., 1980), showing a near identity of these two phage (there are only 59 nucleotide differences). Regulatory units for replication, transcription, and translation are in their essential parts identical in all three phage.

Becker, K. M., C. L. Moe, et al. (2000). "Transmission of Norwalk virus during football game." N Engl J Med 343(17): 1223-7.
	BACKGROUND: During a college football game in Florida, diarrhea and vomiting developed in many of the members of a North Carolina team. The next day, similar symptoms developed in some of the players on the opposing team. METHODS: We interviewed those who ate the five meals served to the North Carolina team before the game and some of the players on the opposing team who became ill. Patients with primary cases were members or staff of the team who had vomiting or diarrhea at least 10 hours after but no more than 50 hours after eating a box lunch served the day before the game. Patients with secondary cases had a later onset of symptoms or had symptoms without having eaten the box lunch. Stool samples were examined by electron microscopy and by a reverse-transcription-polymerase-chain-reaction (RT-PCR) assay. RESULTS: The two football teams shared no food or beverages and had no contact off the playing field. Of five meals served to the North Carolina team before the game, only the box lunch was associated with a significant risk of illness (relative risk of illness, 4.1; 95 percent confidence interval, 1.6 to 10.0). The rate of attack among those who ate the box lunch was 62 percent. There were 11 secondary cases among the members and staff of the North Carolina team and 11 such cases among the Florida players. All four stool samples obtained from North Carolina patients were positive for Norwalk-like virus on electron microscopy. All four samples as well as one of two stool samples from players on the Florida team were positive for a Norwalk-like virus of genogroup I on RT-PCR assay; the RT-PCR products had identical sequences. CONCLUSIONS: This investigation documents person-to-person transmission of Norwalk virus among players during a football game. Persons with acute gastroenteritis should be excluded from playing contact sports.

Bedford, A. J., G. Williams, et al. (1978). "Virus accumulation by the rock oyster Crassostrea glomerata." Appl Environ Microbiol 35(6): 1012-8.
	The accumulation of virus by the New Zealand rock oyster Crassostrea glomerata has been studied in a static seawater system using radioactively labeled reovirus type III and Semliki Forest virus. The uptake of virus was found to be less rapid than for the bacterium Escherichia coli and to be unaffected by the presence of the marine alga Dunaliella primolecta in the seawater. Accumulation was dependent on virus concentration, with saturation achieved at 4 X 10(10) reovirus particles per oyster, implying that an oyster possesses a large but finite number of sites for virus adsorption. When the rates of uptake of two viruses of similar size but differing surface properties were compared, the rate of accumulation of the lipoprotein-enveloped Semliki Forest virus was found to be less than that for the protein-enclosed reovirus. This observation, together with the finding that the oyster shell has a strong affinity for virus, suggests that surface properties, rather than size, are the principal factors governing the accumulation of viruses by filter-feeding marine bivalves.

Beekwilder, J., R. Nieuwenhuizen, et al. (1996). "An oligonucleotide hybridization assay for the identification and enumeration of F-specific RNA phages in surface water." Journal of Applied Bacteriology 80(2): 179-186.
	F-specific RNA phages can be used as model organisms for enteric viruses to monitor the effectiveness of sewage treatment, and to assess the potential contamination of surface water with these viruses. In this paper a method is described which identifies RNA phages quantitatively by a plaque hybridization assay. Oligonucleotide probes were developed that can assign phages to their phylogenetic subgroups. Such a distinction is important, since some subgroups preferentially occur in sewage of human origin, while others tend to be associated with animal wastewater. The method has been tested on a large number of isolates and represents an improvement in time and reliability over the previously used serological classification.

Beekwilder, M. J., R. Nieuwenhuizen, et al. (1995). "Secondary structure model for the last two domains of single-stranded RNA phage Q beta." J Mol Biol 247(5): 903-17.
	We have determined the nucleotide sequence of three positive single-stranded RNA coliphages and have used this information, together with the known sequences of the related phages Q beta and SP, to construct a secondary structure model for the two distal domains of Q beta RNA. The 3' terminal domain, which is about 100 nucleotides long, contains most of the 3' untranslated region and folds into four short, regular hairpins. The adjacent 3' replicase domain contains about 1100 nucleotides. Hairpins in this protein-coding domain are much longer and more irregular than in the 3' untranslated region. Both domains are defined by long-distance interactions. The secondary structure is not a collection of hairpin structures connected by single-stranded regions. Rather, the RNA stretches between the stem-loop structures are all involved in an extensive array of long-distance interactions that contract the molecule to a rigid structure in which all hairpins are predicted to have a fixed position with respect to each other. A general feature of the model is that helices tend to be organized in four-way junctions with little or no unpaired nucleotides between them. As a result, there is a potential for coaxial stacking of adjacent stems. The essential features of the model are supported by the S1 nuclease cleavage pattern. Viral RNA sequences are strongly constrained by their coding function. As a result, structural evolution by simple base-pair substitution is not always possible, as this usually requires the juxtaposition of the codon wobble positions in stems. Rather, we often observe co-ordinate base substitutions that maintain the stem, but tend to change the position at which bulges or internal loops are found. Structures that differ in this way are apparently equally fit. Also, the relative position of hairpin loops can shift several nucleotides through an alignment based on maximal sequence identity i.e. amino acid homology. The fact that these structural irregularities do not occur at the 3' untranslated region suggests indeed that the coding function of the RNA constrains the secondary structure. Hairpins with the stable tetraloop motif GNRA and UNCG or their complement are over-represented. This suggests their involvement in segregation of plus and minus strand. The genome of the coliphages contains a well-defined high affinity binding site for the coat protein, which serves to suppress replicase translation and also acts as a nucleation point in capsid formation. Close to the 3' end we find an additional conserved helix that meets the described consensus criteria for coat-protein binding.

Begara-McGorum, I., L. Gonzalez, et al. (2002). "Vacuolar lesion profile in sheep scrapie: factors influencing its variation and relationship to disease-specific PrP accumulation." J Comp Pathol 127(1): 59-68.
	Detailed neuropathological examination for vacuolar lesions was performed on the brains of 42 sheep with clinical signs compatible with scrapie. The sheep were grouped according to their breed (Poll-Dorset, Cheviot, Welsh Mountain, Shetland and Suffolk), their PrP genotype at codons 136, 154 and 171 (VRQ/VRQ, VRQ/ARQ, VRQ/ARR and ARQ/ARQ) and the type of infection (experimental infection with SSBP/1, or natural disease). Twenty-two neuroanatomical sites from seven brain regions were examined for vacuolation in the neuropil and five sites at the level of the obex were examined for intraneuronal vacuolation. In 36 sheep, immunohistochemical examination for disease-specific PrP (PrP(d)) accumulation had also been performed in the same brain regions in an earlier study. The magnitude of total neuropil vacuolation was highest in the naturally affected ARQ/ARQ Suffolk sheep and lowest in the experimentally infected VRQ/VRQ Cheviot sheep and VRQ/ARR Poll-Dorset sheep. The severity of neuropil vacuolation at nine of the 22 neuroanatomical sites examined was used to generate a vacuolar lesion profile, which showed variations between the different sheep groups. These variations could be attributed to both PrP genotype and sheep breed and also possibly to scrapie agent; there was, however, considerable individual variation in lesion profile within sheep groups. All groups showed a similar ratio of neuropil vacuolation to neuronal vacuolation at the level of the obex. Although a positive correlation between neuropil vacuolation and PrP(d) deposition was generally observed, it was low except for the astrocyte-associated pattern of PrP(d) accumulation. The study suggests that vacuolar lesion profiles in sheep are affected by several factors and, by comparison with lesion profiles in mice, are of no more than limited value for discriminating between scrapie strains.

Behan, P. O., W. M. Behan, et al. (1993). "Enteroviruses and postviral fatigue syndrome." Ciba Found Symp 173: 146-54; discussion 154-9.
	Postviral fatigue syndrome (PFS) occurs both in epidemics and sporadically. Many of the original epidemics were related to poliomyelitis outbreaks which either preceded or followed them. The core clinical symptoms are always the same: severe fatigue made worse by exercise, myalgia, night sweats, atypical depression and excessive sleep. The other common symptoms include dysequilibrium disorders and irritable bowel syndrome. We have detected enteroviral genome sequences in muscle biopsies from cases of PFS, using specific enteroviral oligonucleotide primers in the polymerase chain reaction (PCR). In addition, whole virus particles can be demonstrated in PCR-positive muscle, using solid-phase immuno-electron microscopy. An increase in the number and size of muscle mitochondria was found in 70% of PFS cases, suggesting an abnormality in metabolic function. Evidence of hypothalamic dysfunction was present, particularly involving 5-hydroxytryptamine metabolism. A putative model of PFS, based on persistent enteroviral infection in laboratory mice, revealed resolving inflammatory lesions in muscle with, however, a marked increase in the production of certain cytokines in the brain. This model may help to explain the pathogenesis of PFS.

Beijerinck, M. W. (1964). Concerning a contagium vivum fluidum as cause of the spot disease of tobacco leaves. Selected papers on virology. N. Hahon. Englewood Cliffs, New Jersey, Prentice Hall Inc.: 52-63.
	
Bell, B. P., C. N. Shapiro, et al. (1998). "The diverse patterns of hepatitis A epidemiology in the United States-implications for vaccination strategies." J Infect Dis 178(6): 1579-84.
	Hepatitis A is the most frequently reported vaccine-preventable disease in the United States. Hepatitis A incidence and risk factors during 1983-1995 were examined among cases reported to the study's Sentinel Counties: Denver County, Colorado; Pierce County, Washington; Jefferson County, Alabama; and Pinellas County, Florida. Of 4897 serologically confirmed cases, 611 patients (13%) were hospitalized and 9 (0.2%) died. The average incidence was 14.7/100, 000 (range, 0.6-100.7/100,000, depending on county and year). The frequency of reported sources of infection varied by county, but the largest single group overall (52%) did not report a source. During 3-year communitywide outbreaks in Denver (1991-1993) and Pierce (1987-1989) Counties, rates increased 4- and 13-fold, respectively, and increased in all age, racial/ethnic, and risk groups. During communitywide outbreaks, hepatitis A is not limited to specific risk groups; sustained nationwide reductions in incidence are more likely to result from routine childhood vaccination than from targeted vaccination of high-risk groups.

Bell, D., S. Roberton, et al. (2004). "Animal origins of SARS coronavirus: possible links with the international trade in small carnivores." Philos Trans R Soc Lond B Biol Sci 359(1447): 1107-14.
	The search for animal host origins of severe acute respiratory syndrome (SARS) coronavirus has so far remained focused on wildlife markets, restaurants and farms within China. A significant proportion of this wildlife enters China through an expanding regional network of illegal, international wildlife trade. We present the case for extending the search for ancestral coronaviruses and their hosts across international borders into countries such as Vietnam and Lao People's Democratic Republic, where the same guilds of species are found on sale in similar wildlife markets or food outlets. The three species that have so far been implicated, a viverrid, a mustelid and a canid, are part of a large suite of small carnivores distributed across this region currently overexploited by this international wildlife trade. A major lesson from SARS is that the underlying roots of newly emergent zoonotic diseases may lie in the parallel biodiversity crisis of massive species loss as a result of overexploitation of wild animal populations and the destruction of their natural habitats by increasing human populations. To address these dual threats to the long-term future of biodiversity, including man, requires a less anthropocentric and more interdisciplinary approach to problems that require the combined research expertise of ecologists, conservation biologists, veterinarians, epidemiologists, virologists, as well as human health professionals.

Bellander, J. (1941). "Observations on an epidemic of jaundice during 1939-1940." Svenska Lakartidningen 38: 1169-1181.
	
Beller, M. (1992). "Hepatitis A outbreak in Anchorage, Alaska, traced to ice slush beverages." West. J. Med. 156(6): 624-627.
	The Alaska Department of Health and Social Services investigated a community outbreak of hepatitis A in Anchorage. A total of 57 persons who had hepatitis A between June and September 1988 were studied. Patients ranged from 1 to 54 years of age. A market was implicated as the source of the outbreak. An employee who prepared beverage mixtures in a bathroom was a contact of a person who had had hepatitis A 2 months before the outbreak; the employee was reported to have been jaundiced 3 to 4 weeks before the peak of the outbreak. The administration of immune globulin had an efficacy of 100% (95% confidence limits 69, 100%) in preventing hepatitis A among household contacts of primary cases. Similar beverages are sold by convenience markets and many other businesses nationwide. It is important to ensure that safe food-handling practices are followed by such establishments.

Beller, M., A. Ellis, et al. (1997). "Outbreak of viral gastroenteritis due to a contaminated well. International consequences." Jama 278(7): 563-8.
	CONTEXT: Small round-structured viruses (SRSVs) are known to cause viral gastroenteritis, but until now have not been confirmed in the implicated vehicle in outbreaks. OBJECTIVE: Investigation of a gastroenteritis outbreak. DESIGN: After applying epidemiologic methods to locate the outbreak source, we conducted environmental and laboratory investigations to elucidate the cause. SETTING: Tourists traveling by bus through Alaska and the Yukon Territory of Canada. PARTICIPANTS: Staff of a restaurant at a business complex implicated as the outbreak source, convenience sample of persons on buses that had stopped there, and bus employees. MAIN OUTCOME MEASURES: Odds ratios (ORs) for illness associated with exposures. Water samples from the restaurant and stool specimens from tourists and restaurant staff were examined by nucleic acid amplification using reverse transcription polymerase chain reaction and sequencing of viral amplification products. RESULTS: The itineraries of groups of tourists manifesting vomiting or diarrhea were traced back to a restaurant where buses had stopped 33 to 36 hours previously. Water consumption was associated with illness (OR, 5.3; 95% confidence interval [CI], 2.3-12.6). Eighteen of 26 employees of the business complex were ill; although not the index case, an employee ill shortly before the outbreak lived in a building connected to a septic pit, which was found to contaminate the well supplying the restaurant's water. Genotype 2/P2B SRSV was identified in stool specimens of 2 tourists and 1 restaurant employee. Stools and water samples yielded identical amplification product sequences. CONCLUSIONS: The investigation documented SRSVs in a vehicle epidemiologically linked to a gastroenteritis outbreak. The findings demonstrate the power of molecular detection and identification and underscore the importance of fundamental public health practices such as restaurant inspection, assurance of a safe water supply, and disease surveillance.

Belliot, G., A. Lavaux, et al. (2008). "Use of murine norovirus as a surrogate to evaluate resistance of human norovirus to disinfectants." Appl Environ Microbiol 74(10): 3315-8.
	Murine norovirus (MNV) was used as a surrogate to study resistance of human norovirus to disinfectants used in hospitals. MNV was sensitive to alcohol, alcohol hand rubs, bleach, and povidone iodine-based disinfectant. Real-time reverse transcription-PCR results indicated that the presence of viral RNA did not correlate with the presence of infectious virus.

Belliot, G., H. Laveran, et al. (1997). "Capsid protein composition of reference strains and wild isolates of human astroviruses." Virus Res 49(1): 49-57.
	Astroviruses are small RNA viruses that are frequently associated with gastroenteritis in humans and animals. Despite much work on the genetic analysis of astrovirus strains, little progress has been made in the characterization of the proteins composing mature virions. We have analyzed the capsid protein composition of the reference strains and several wild isolates of human astroviruses using high-resolution polyacrylamide gradient gels. For reference strains of the seven serotypes analyzed, a consistent pattern of three infection-specific proteins--designated P1, P2, and P3 -was generally observed. The strains could be divided into two groups, based upon the reactivity of these proteins in immune precipitation assays that used homologous rabbit serum. One group included reference types 1 4 for which all three proteins were precipitated by homologous rabbit sera; for the other group, types 5 7, only proteins P2 and P3 were precipitated. When wild isolates from around the world were compared to the reference strains, a correlation between genetic type and the pattern of protein sizes and immune reactivity was observed for strains of the common types (1-4). Strains of types 2 and 4 consistently exhibited P3 proteins larger than those of types 1 and 3. Unusual patterns of proteins or immune reactivity were detected in strains of types 5-7, indicating that there may be incomplete processing of the capsid precursor during growth in cell culture.

Belliot, G., H. Laveran, et al. (1997). "Detection and genetic differentiation of human astroviruses: phylogenetic grouping varies by coding region." Arch Virol 142(7): 1323-34.
	Astroviruses are single-stranded, positive-sense RNA viruses that are associated with gastroenteritis in humans and animals. We describe a reverse transcription-polymerase chain reaction (RT-PCR) assay using primers targeted to a nonstructural protein coding region that allowed sensitive detection and genetic typing of representative strains of seven astrovirus serotypes. Phylogenetic analysis of the nucleotide sequences of PCR products from the reference strains and several wild isolates indicated two distinct genogroups of sequences in open reading frame 1a (ORF 1a). These genogroups correlated with serotype: genogroup A included strains of types 1 to 5, while genogroup B included strains of types 6 and 7. This phylogenetic arrangement differs from the nearly equidistant clustering of serotypes seen when comparing nucleotide sequences from either ORF 1b or ORF 2. It is possible that recombination was responsible for the observed difference in genetic relationships.

Belliot, G., H. Laveran, et al. (1997). "Outbreak of gastroenteritis in military recruits associated with serotype 3 astrovirus infection." J Med Virol 51(2): 101-6.
	A serotype 3 astrovirus was identified in stool samples from an outbreak of acute gastroenteritis that occurred among military recruits in France. Sixteen stools samples and eight pairs of acute- and convalescent-phase serum were collected from affected individuals. Astrovirus was detected in two stool samples by electron microscopy and in four stool samples by reverse transcriptase-polymerase chain reaction (RT-PCR). Seroconversion to the astrovirus present in one stool was detected in seven patients by using solid-phase immune electron microscopy (SPIEM) and dot blot. For three patients, the serological results were consistent with the PCR results, indicating that astrovirus was a cause of gastroenteritis in these young adults. This study describes the characterization of the serotype 3 astrovirus associated with this outbreak. The virus has a buoyant density in cesium chloride of 1.365 gm/ml and contains two proteins immuno-precipitated with rabbit serum. Only the larger protein was recognized by immunoblotting using a convalescent-phase human serum. The protein composition of this virus differs from that reported for serotype 1 astrovirus, indicating heterogeneity in the capsid composition among astrovirus serotypes.

Belliot, G., J. S. Noel, et al. (2001). "Characterization of capsid genes, expressed in the baculovirus system, of three new genetically distinct strains of "Norwalk-like viruses"." J Clin Microbiol 39(12): 4288-95.
	"Norwalk-like viruses" (NLVs), members of a newly defined genus of the family Caliciviridae, are the most common agents of outbreaks of gastroenteritis in the United States. Two features of NLVs have hindered the development of simple methods for detection and determination of serotype: their genetic diversity and their inability to grow in cell culture. To assess the immune responses of patients involved in outbreaks of gastroenteritis resulting from infection with NLVs, we previously used recombinant-expressed capsid antigens representing four different genetic clusters, but this panel proved insufficient for detection of an immune response in many patients. To extend and further refine this panel, we expressed in baculovirus the capsid genes of three additional genetically distinct viruses, Burwash Landing virus (BLV), White River virus (WRV), and Florida virus. All three expressed proteins assembled into virus-like particles (VLPs) that contained a full-length 64-kDa protein, but both the BLV and WRV VLPs also contained a 58-kDa protein that resulted from deletion of 39 amino acids at the amino terminus. The purified VLPs were used to measure the immune responses in 403 patients involved in 37 outbreaks of acute gastroenteritis. A majority of patients demonstrated a fourfold rise in the titer of immunoglobulin G to the antigen homologous to the outbreak strain, but most seroconverted in response to other genetically distinct antigens as well, suggesting no clear pattern of type-specific immune response. Further study of the antigenicity of the NLVs by use of VLPs should allow us to design new detection systems with either broader reactivity or better specificity and to define the optimum panel of antigens required for routine screening of patient sera.

Belliot, G. M., R. L. Fankhauser, et al. (2001). "Characterization of "Norwalk-like viruses" and astroviruses by liquid hybridization assay." J Virol Methods 91(2): 119-30.
	"Norwalk-like viruses" (NLVs) and human astroviruses are causative agents of gastroenteritis in all age-groups. The typing of these agents is generally done by nucleotide sequencing, blot hybridization, or enzyme immunoassay. These techniques are expensive, time-consuming, and sometimes require scarce reagents, which limits the typing of NLVs and astroviruses to a few reference laboratories. This report describes a liquid hybridization assay that uses broadly reactive probes whose sequences are based on data from specimens in collections available at CDC and GenBank. Two astrovirus genogroup-specific probes were designed and tested successfully on 26 wild strains from all serotypes. Fourteen GII and 16 GI representative NLV strains were typed without cross-hybridization by using P1B- and P2A-specific probes, described previously, and new P2B- and P1A-specific probes. Analysis of the specificity of the probes, the effect of the mismatches during hybridization, and the sensitivity of hybridization assay demonstrates this method to be a rapid and simple technique for molecular typing of NLVs and preliminary characterization of astroviruses.

Belnap, D. M., B. M. McDermott, Jr., et al. (2000). "Three-dimensional structure of poliovirus receptor bound to poliovirus." Proc Natl Acad Sci U S A 97(1): 73-8.
	Poliovirus initiates infection by binding to its cellular receptor (Pvr). We have studied this interaction by using cryoelectron microscopy to determine the structure, at 21-A resolution, of poliovirus complexed with a soluble form of its receptor (sPvr). This density map aided construction of a homology-based model of sPvr and, in conjunction with the known crystal structure of the virus, allowed delineation of the binding site. The virion does not change significantly in structure on binding sPvr in short incubations at 4 degrees C. We infer that the binding configuration visualized represents the initial interaction that is followed by structural changes in the virion as infection proceeds. sPvr is segmented into three well-defined Ig-like domains. The two domains closest to the virion (domains 1 and 2) are aligned and rigidly connected, whereas domain 3 diverges at an angle of approximately 60 degrees. Two nodules of density on domain 2 are identified as glycosylation sites. Domain 1 penetrates the "canyon" that surrounds the 5-fold protrusion on the capsid surface, and its binding site involves all three major capsid proteins. The inferred pattern of virus-sPvr interactions accounts for most mutations that affect the binding of Pvr to poliovirus.

Belov, G. A., P. V. Lidsky, et al. (2004). "Bidirectional increase in permeability of nuclear envelope upon poliovirus infection and accompanying alterations of nuclear pores." J Virol 78(18): 10166-77.
	Poliovirus and some other picornaviruses trigger relocation of certain nuclear proteins into the cytoplasm. Here, by using a protein changing its fluorescence color with time and containing a nuclear localization signal (NLS), we demonstrate that the poliovirus-triggered relocation is largely due to the exit of presynthesized nuclear protein into the cytoplasm. The leakiness of the nuclear envelope was also documented by the inability of nuclei from digitonin-permeabilized, virus-infected (but not mock-infected) cells to retain an NLS-containing derivative of green fluorescent protein (GFP). The cytoplasm-to-nucleus traffic was also facilitated during infection, as evidenced by experiments with GAPDH (glyceraldehyde-3-phosphate dehydrogenase), cyclin B1, and an NLS-lacking derivative of GFP, which are predominantly cytoplasmic in uninfected cells. Electron microscopy demonstrated that a bar-like barrier structure in the channel of the nuclear pores, seen in uninfected cells, was missing in the infected cells, giving the impression of fully open pores. Transient expression of poliovirus 2A protease also resulted in relocation of the nuclear proteins. Lysates from poliovirus-infected or 2A-expressing cells induced efflux of 3xEGFP-NLS from the nuclei of permeabilized uninfected cells. This activity was inhibited by the elastase inhibitors elastatinal and N-(methoxysuccinyl)-L-alanyl-L-alanyl-L-prolyl-L-valine chloromethylketone (drugs known also to be inhibitors of poliovirus protease 2A), a caspase inhibitor zVAD(OMe), fmk, and some other protease inhibitors. These data suggest that 2A elicited nuclear efflux, possibly in cooperation with a zVAD(OMe).fmk-sensitive protease. However, poliovirus infection facilitated nuclear protein efflux also in cells deficient in caspase-3 and caspase-9, suggesting that the efflux may occur without the involvement of these enzymes. The biological relevance of nucleocytoplasmic traffic alterations in infected cells is discussed.

Bemiss, J. A., M. M. Logan, et al. (1989). "A method for the enumeration of poliovirus in selected molluscan shellfish." J Virol Methods 26(2): 209-17.
	A virus extraction procedure was developed and evaluated on five commercially important molluscan shellfish species: Crassostrea virginica (Eastern oyster), Mya arenaria (softshell clam), Mytilus edulis (blue mussel), Mercenaria mercenaria (hardshell clam), and Crassostrea gigas, (Pacific oyster). Shellfish tissue homogenates were spiked with poliovirus, extracted, and plaque assayed. Mean virus recoveries were: C. virginica, 63.8%; M. arenaria, 42.1%; M. edulis, 67.3%; M. mercenaria, 48.3%; and C. gigas 10.1%. Shellfish were also allowed to accumulate poliovirus from spiked seawater (10 to 20 PFU/ml of water) over 48 to 72 h. The results indicate that poliovirus could be extracted from four shellfish species exposed to near environmental levels of virus. Virus recoveries per gram of tissue were: M. arenaria, 11.7 PFU; M. mercenaria, 26.0 PFU; M. edulis, 21.5 PFU; and C. virginica, 2.0 PFU. The results of this study indicate that the procedure is effective in extracting ingested viruses from several shellfish species. This procedure may have practical application for enumeration of enteric viruses in environmental samples.

Bemiss, J. A., M. M. Logan, et al. (1990). "A method for the enumeration of poliovirus in selected molluscan shellfish." Journal of Virological Methods 26: 209-218.
	
Bendinelli, M. and A. Ruschi (1969). "Isolation of human enterovirus from mussels." Appl Microbiol 18(3): 531-2.
	Mussels maintained in sea water heavily polluted with domestic raw sewage have been found to harbor human enteroviruses.

Beneduce, F., A. Ciervo, et al. (1999). "Mapping of protein domains of hepatitis A virus 3AB essential for interaction with 3CD and viral RNA." Virology 264(2): 410-21.
	The small hydrophobic protein 3AB of the picornaviruses, encompassing the replication primer 3B, has been suggested to anchor the viral replication complex to membranes. For hepatitis A virus (HAV) 3AB, we have previously demonstrated its ability to form stable homodimers, to bind to membranes, and to interact specifically with RNA, implicating its multiple involvement in viral replication. In the present report, we show that HAV 3AB additionally interacts with HAV protein 3CD, a feature also described for the corresponding polypeptide of poliovirus. By assessing the interactions of three deletion mutants, distinct domains of HAV 3AB were mapped. The hydrophobic domain and the 3B moiety were found to be essential for the 3AB interaction with 3CD. Both electrostatic and hydrophobic forces are involved in this interaction. The cluster of charged amino acid residues at the C terminus of 3A seems to determine the specificity of 3AB interaction with RNA structures formed at either terminus of the HAV genome. Furthermore, our data implicate that 3A can interact with HAV RNA. Compared with poliovirus 3AB, which by itself is a nonspecific RNA-binding protein, HAV 3AB specifically recognizes HAV RNA structures that might be of relevance for initiation of viral RNA replication.

Beneduce, F., A. Ciervo, et al. (1997). "Site-directed mutagenesis of hepatitis A virus protein 3A: effects on membrane interaction." Biochim Biophys Acta 1326(1): 157-65.
	Due to a stretch of hydrophobic amino acids, protein 3A of hepatitis A virus (HAV) has been suggested to act as a membrane anchor or a carrier of the genome-linked protein 3B (VPg) during viral RNA synthesis. Mutagenesis analysis was performed in order to elucidate the role of the N- and C-terminal tracts of protein 3A in cell membrane interaction. Expression of the mutated proteins in E. coli cells demonstrated that the presence of positively charged residues at the C-terminus is not required for membrane anchoring. Changes in the primary sequence involving charged amino acids at the N- and C-termini critically influenced the ability of the protein 3A of a cytopathic strain of HAV to change bacterial membrane permeability. This result demonstrates the strict correlation between the structure and pore-forming potential of HAV protein 3A.

Beneduce, F., Y. Kusov, et al. (2002). "Chimeric hepatitis A virus particles presenting a foreign epitope (HIV gp41) at their surface." Antiviral Res 55(2): 369-77.
	Hepatitis A virus (HAV) protein 2A has been demonstrated to be involved in virus morphogenesis and suggested to be located on the surface of the particle. To determine whether this protein can function as a target structure to harbor and expose foreign epitopes on HAV particles, a full-length HAV cDNA, containing a seven amino acid stretch of human immunodeficiency virus type 1 (HIV-1) envelope protein gp41, was constructed. Following vaccinia virus MVA-T7-mediated expression of the cDNA in COS7 and Huh-T7 cells, chimeric HAV particles, exposing the foreign epitope gp41 on their surface, were produced. These particles were found to be empty capsids (70S), as judged by immunospecific enzyme linked immunosorbent assay (ELISA) on sucrose gradient fractions and immunoelectron microscopy. The immunological detection of VP1-2A harboring the gp41 epitope of HIV suggests that the 2A domain of HAV is suitable to present foreign antigenic epitopes.

Beneduce, F., G. Pisani, et al. (1995). "Complete nucleotide sequence of a cytopathic hepatitis A virus strain isolated in Italy." Virus Res 36(2-3): 299-309.
	The molecular basis of the cytopathic effect induced in cell culture by some hepatitis A virus (HAV) strains and variants has not been determined. In order to assess the molecular mechanism(s) underlying this particular phenotype the genome of an Italian cytopathic isolate (strain FG) was sequenced from cDNAs obtained by RT-PCR. Sequence analysis revealed the presence of mutations common to either adapted or cytopathic variants of HAV. In particular, amino acid deletions in proteins VP1 and 3A were detected. Expression of protein 3A in E. coli showed that the N-terminal deletion renders this protein toxic to bacteria.

Benton, W. H. and C. J. Hurst (1986). "Evaluation of mixed cell types and 5-iodo-2'-deoxyuridine treatment upon plaque assay titers of human enteric viruses." Appl Environ Microbiol 51(5): 1036-40.
	Four continuous cell lines, BGM, L-132, HEL-299, and RD, were compared both when cultured separately and as mixtures for use in plaque assay titrations of human adenovirus 1 and six human enterovirus serotypes. The effect of incubating these cell cultures in media containing 5-iodo-2'deoxyuridine (IDU) prior to inoculation with virus was also studied. The use of mixed-cell cultures revealed cell line-dependent synergistic effects as well as inhibitory effects. These effects were strongly virus dependent. In particular, enterovirus 69 did not form plaques on any of the four cell lines when cultured independently. However, it did form plaques on nearly all of the cell lines when cultured as mixtures. Contrary to this effect, when BGM cells were used in combination with the other cell lines, plaque counts for adenovirus 1 were greatly reduced. The effect of IDU pretreatment was also virus and cell line specific and enabled some viruses to form plaques on cell lines when they otherwise would not. Overall, IDU pretreatment resulted in an approximate twofold increase in plaque titers over those obtained without treatment.

Benton, W. H. and R. L. Ward (1982). "Induction of cytopathogenicity in mammalian cell lines challenged with culturable enteric viruses and its enhancement by 5-iododeoxyuridine." Appl Environ Microbiol 43(4): 861-8.
	Cultures of 17 established cell lines were tested against 105 enteric virus types for capacity to support viral replication as indicated by cytopathogenic effect production. Enhancement of susceptibility by treatment of the cells with 5-iododeoxyuridine was evaluated in parallel with untreated cells. Cytopathogenic effect was produced in two or more cell lines by every virus tested except six strains of group A coxsackie virus. No cell line was found to be susceptible to these six virus types. In general, treatment with 5-iododeoxyuridine provided a more rapid onset of cytopathogenic effect in susceptible cells and in some instances resulted in refractory cells becoming permissive to viral replication. The use of 5-iododeoxyuridine allowed two human embryonic lines (HEL-299 and L-132), in combination, to be susceptible to all but the six group A coxsackie virus strains.

Berg, D. E., M. A. Kohn, et al. (2000). "Multi-state outbreaks of acute gastroenteritis traced to fecal-contaminated oysters harvested in Louisiana." J Infect Dis 181 Suppl 2: S381-6.
	Norwalk-like viruses (NLVs), or small round structured viruses, are known to cause acute gastroenteritis associated with eating contaminated shellfish. Between 1993 and 1996, three oyster-related gastroenteritis outbreaks attributed to NLV occurred in Louisiana. Intensive trace-back and environmental investigations revealed that the overboard disposal of sewage by oyster harvesters into oyster-bed waters was the most likely source of contamination in at least two of the outbreaks. The small infectious dose of NLV, the large quantity of virus particles in stool, and the ability of oysters to concentrate virus particles suggest that oyster-related outbreaks will continue unless strong control measures are established. Efforts to halt improper sewage disposal in oyster-harvesting waters, including overboard sewage discharge, must be undertaken if future outbreaks are to be prevented.

Berg, G. (1967). Transmission of viruses by the water route. New York, Interscience (John Wiley & Sons).
	
Berg, G., D. Berman, et al. (1966). "A sensitive quantitative method for detecting small quantities of virus in large volumes of water." American Journal of Epidemiology 83(2): 196-203.
	
Berg, G., N. A. Clarke, et al. (1962). "Interrelationships among ECHO virus types 1,8, and 12." J. Bacteriol. 83: 556-560.
	Berg, Gerald (Robert A. Taft Sanitary Engineering Center, Cincinnati, Ohio), Norman A. Clarke, and Paul W. Kabler. Interrelationships among ECHO virus types 1, 8, and 12. J. Bacteriol. 83:556-560. 1962.-Antigenic relationships among ECHO 1, 8, and 12 viruses were investigated. Three strains of ECHO 1 virus, one of which had been purified, could not be differentiated by neutralization tests. Antiserums produced with these three strains neutralized ECHO 12 virus. The neutralizing material, absent from preimmunization serums, was not absorbed by rhesus kidney cells, was heat-stable, and, therefore, may be viral antibody. Reciprocal neutralization was achieved with all three types. Disagreement of these data with those published by others is discussed.

Berg, G., D. R. Dahling, et al. (1978). "Validity of fecal coliforms, total coliforms, and fecal streptococci as indicators of viruses in chlorinated primary sewage effluents." Applied and Environmental Microbiology 36(6): 880-884.
	Quantities of combined chlorine that usually destroyed more than 99.999% of the indigenous fecal coliforms, total coliforms, and fecal streptococci in primary sewage effluents destroyed only 85 to 99% of the indigenous viruses present. Viruses were recovered from five of eight chlorinated primary effluents from which fecal coliforms were not recovered by standard most-probable-number procedures. The limited volumes of such chlorinated effluents that can be tested for indicator bacteria with currently available multiple-tube and membrane filter techniques restrict the value of fecal coliforms, fecal streptococci, and even total coliforms as indicators of viruses in these effluents. Although fecal coliforms and fecal streptococci are useful indicators of viruses in effluents from which these bacteria are recovered, the absence of these bacteria and even total coliforms from disinfected effluents (in standard tests) does not assure that viruses are also absent. 

Berg, G. and G. Sullivan (1988). "Optimum Ph Levels for Eluting Enteroviruses from Sludge Solids with Beef Extract." Applied & Environmental Microbiology 54(7): 1880-1881.
	This study demonstrates that elution of enteroviruses from a mixture of primary- and activated-sludge solids with beef extract at pH 9.2 .+-. 0.2 may be less efficient than elution with beef extract at pH 7.2 .+-. 0.2 and that elution of enteroviruses from extended-aeration-sludge solids with beef extract is at best no more efficient at pH 9.2 .+-. 0.2 than at pH 7.2 .+-. 0.2. Thus, the common practice of adjusting the pH of beef extract used for eluting enteroviruses from the natural neutral level of the elutant to alkaline levels is unnecessary and probably undesirable.

Berg, G., G. Sullivan, et al. (1988). "Low-Temperature Stability of Viruses in Sludges." Applied & Environmental Microbiology 54(3): 839-841.
	Enteroviruses survived for up to 38 days without diminishing in numbers in extended-aeration sludges maintained at 5.degree.C. In oxidation ditch sludges similarly maintained, enteroviruses survived for up to 17 days without diminishing in numbers. The pHs of the sludges in this study were well inside the pH 6 to 8 corridor in which destruction of enteroviruses by the detergents and ammonia present in sludges reportedly does not occur. Unexplained, however, was the survival of large numbers of enteroviruses in sludges at pH 3.5, a pH at which some anionic detergents commonly present in sewage are rapidly virucidal. The long survival of enteroviruses in these sludges at 5.degree.C indicates that such sludges can probably be stored under refrigeration in the laboratory for extended periods while awaiting processing without suffering significant losses in enterovirus numbers.

Berg, G. E. (1978). Indicators of Viruses in Water and Food. Ann Arbor, Michigan, Ann Arbor Science.
	
Berger, R. and M. Just (1992). "Vaccination against hepatitis A: control 3 years after the first vaccination." Vaccine 10(4): 295.
	not available

Berke, T., B. Golding, et al. (1997). "Phylogenetic analysis of the caliciviruses." Journal of Medical Virology 52(4): 419-424.
	A phylogenetic portrait of the genus Calicivirus in the family Caliciviridae was developed based upon published sequences and newly characterized calicivirus (CV) strains, including additional Sapporo-like HuCV strains in pediatric diarrhea stool specimens from South Africa, the United Kingdom, and the United States. Distance and parsimony methods were applied to nucleotide and amino acid sequences of human and animal calicivirus 3D RNA-dependent RNA polymerase ( approximates 470nt) and capsid hypervariable regions ( approximates 1,200nt) to generate phylogenetic trees. Pairwise amino acid identity in the 3D region among the Sapporo-like strains ranged from 61% to 100%. Human and animal caliciviruses (HuCVs and AnCVs) separated into five genogroups: small round-structured viruses (SRSV), Sapporo-like, and hepatitis E virus (HEV)-like HuCVs and rabbit-, and vesicular exanthema of swine virus (VESV)-like AnCVs, each with a distinct genome organization. Each genogroup, including the Sapporo-like HuCVs, subdivided further into subgenogroups. The capsid region trees had higher levels of confidence than the 3D region trees and limited conclusions about genogroups could be drawn from the 3D region analyses. This analysis suggested that CVs include five potential virus subfamilies.

Berke, T. and D. O. Matson (2000). "Reclassification of the Caliciviridae into distinct genera and exclusion of hepatitis E virus from the family on the basis of comparative phylogenetic analysis." Arch Virol 145(7): 1421-36.
	Caliciviridae and Picornaviridae belong to the same subphylum and genera within Picornaviridae are well characterized. Until 1998, Caliciviridae included one genus Calicivirus, containing strains with distinct structural and genomic features. Phylogenetic analyses of capsid genes revealed five clusters within Caliciviridae corresponding to differences in genome organization. In order to determine to what taxonomic level these clusters correspond, genomic sequences of caliciviruses, picornavirus prototypes, and two togavirus strains were analyzed. Distance and maximum likelihood methods were used to estimate the phylogenetic relationships among strains. Analysis of the capsid gene revealed separation of five main clusters (Norwalk-like, and Sapporo-like human caliciviruses, hepatitis E virus, vesicular exanthem of swine-like, and lapine caliciviruses) and distances corresponding to those observed among picornavirus genera. Utilizing more conserved (presumed helicase and polymerase) regions for the analyses, only major groups of caliciviruses were separated with confidence, with distances also comparable to those separating picornavirus genera. Analysis in these regions that included togavirus sequences moved HEV strains out of the calicivirus cluster. Our findings support the reclassification of caliciviruses into four genera. The phylogenetic position of hepatitis E virus, by analysis of non-structural genes, is outside of the caliciviruses, in an uncertain taxonomic position.

Berlin, D. L., D. S. Herson, et al. (1999). "Response of pathogenic Vibrio species to high hydrostatic pressure." Appl Environ Microbiol 65(6): 2776-80.
	Vibrio parahaemolyticus ATCC 17802, Vibrio vulnificus ATCC 27562, Vibrio cholerae O:1 ATCC 14035, Vibrio cholerae non-O:1 ATCC 14547, Vibrio hollisae ATCC 33564, and Vibrio mimicus ATCC 33653 were treated with 200 to 300 MPa for 5 to 15 min at 25 degrees C. High hydrostatic pressure inactivated all strains of pathogenic Vibrio without triggering a viable but nonculturable (VBNC) state; however, cells already existing in a VBNC state appeared to possess greater pressure resistance.

Berman, D., G. Berg, et al. (1981). "A method for recovering viruses from sludges." J Virol Methods 3(5): 283-91.
	Primary, activated, and anaerobic mesophilically digested sludges were salted with MgCl2 (divalent cations) or AlCl3 (trivalent cations) and acidified to bind indigenous unadsorbed virions to the sludge solids; the sludges were centrifuged, and the adsorbed virions were eluted from the solids with buffered 10% beef extract. The elution yields with this procedure were superior to those obtained from sludges that had been salted or acidified only. Homogenization of sludges prior to other treatment did not increase the numbers of virions recovered.

Berman, D. and J. C. Hoff (1984). "Inactivation of simian rotavirus SA11 by chlorine, chlorine dioxide, and monochloramine." Applied and Environmental Microbiology 48(2): 317-323.
	The kinetics of inactivation of simian rotavirus SA11 by chlorine, chlorine dioxide, and monochloramine were studied at 5 degrees C with a purified preparation of single virions and a preparation of cell-associated virions. Inactivation of the virus preparations with chlorine and chlorine dioxide was studied at pH 6 and 10. The monochloramine studies were done at pH 8. With 0.5 mg of chlorine per liter at pH 6, more than 4 logs (99.99%) of the single virions were inactivated in less than 15 s. Both virus preparations were inactivated more rapidly at pH 6 than at pH 10. With chlorine dioxide, however, the opposite was true. Both virus preparations were inactivated more rapidly at pH 10 than at pH 6. With 0.5 mg of chlorine dioxide per liter at pH 10, more than 4 logs of the single-virus preparation were inactivated in less than 15 s. The cell-associated virus was more resistant to inactivation by the three disinfectants than was the preparation of single virions. Chlorine and chlorine dioxide, each at a concentration of 0.5 mg/liter and at pH 6 and 10, respectively, inactivated 99% of both virus preparations within 4 min. Monochloramine at a concentration of 10 mg/liter and at pH 8 required more than 6 h for the same amount of inactivation. 

Berman, D., R. Sullivan, et al. (1992). "Effect of the method of preparing monochloramine upon inactivation of MS2 coliphage, Escherichia coli, and Klebsiella pneumoniae." Can J Microbiol 38(1): 28-33.
	Monochloramine prepared in situ by first adding chlorine to a suspension of microorganisms, followed by subsequent addition of ammonia, inactivated the MS2 coliphage more rapidly than did exposure of phage to monochloramine prepared either by adding chlorine to ammonia or by adding chlorine and ammonia simultaneously. The rapid viral inactivation was apparently due to the exposure of MS2 to free chlorine before the addition of ammonia. The average 99% CT value of MS2 when exposed to free chlorine was 1.3 and 1.1 at 5 and 15 degrees C, respectively. The average 99% CT values of MS2 briefly exposed to the combined action of free chlorine followed by the addition of ammonia to form monochloramine in situ were 19.3 and 1.5 at 5 and 15 degrees C, respectively. No 99% CT values were calculated for the inactivation of MS2 with preformed monochloramine because less than 1 log (90%) of inactivation occurred during a 4-h contact time. Inactivation of MS2 by monochloramine was more rapid at 15 than at 5 degrees C and when the chlorine to nitrogen weight ratio was 5:1 compared with 3:1. Monochloramine was a more efficient inactivating agent for the coliforms Escherichia coli and Klebsiella pneumoniae than it was for the MS2 coliphage.

Bernstein, D. I., J. M. Ziegler, et al. (1986). "Rotavirus fecal IgA antibody response in adults challenged with human rotavirus." J Med Virol 20(4): 297-304.
	Our studies of rotavirus challenge in adult volunteers enabled us to evaluate the relationship of pre-existing antirotavirus fecal IgA antibody to infection and illness and to investigate the local response to this infection. No relationship could be found between the pre-existing levels of fecal antirotavirus IgA antibody and protection from infection or illness. A greater than six-fold increase in the level of antibody was seen in 16/19 infected volunteers with determinable increases but in 0/15 controls who received less than the minimal infectious dose of rotavirus. Antibody levels increased rapidly in infected volunteers and were consistent with an anamnestic response. Two of seven volunteers who received an infectious dose of rotavirus but were considered uninfected on the basis of other laboratory methods had greater than or equal to six-fold increases of fecal antibody and one of these experienced symptoms compatible with a rotavirus infection. This finding indicates that an increase in fecal antibody may be a reliable indicator of rotavirus infection even in the absence of detectable shedding or seroconversion.

Berry, E. S., D. E. Skilling, et al. (1990). "New marine calicivirus serotype infective for swine." Am J Vet Res 51(8): 1184-7.
	A new serotype of calicivirus was isolated from California sea lions (Zalophus californianus) with severe vesicular disease. Neutralizing antibodies were found in 27 of 82 (32.9%) serum samples from California sea lions and in 15 of 146 (10.3%) serum samples from Steller sea lions (Eumetopias jubatus) tested. The seropositive animals were widely dispersed along the margins of the eastern Pacific basin, from the Bering Sea to the Santa Barbara Channel. Seropositive samples were found from as early as 1976 through the present time. This new calicivirus serotype, San Miguel sea lion virus type 13, was inoculated into weaned pigs, resulting in induction of severe vesicular disease, which spread to all pigs, including uninoculated pen contacts. Virus was continually shed by most of the pigs throughout the 2-week duration of the experiment.

Bertolotti-Ciarlet, A., S. E. Crawford, et al. (2003). "The 3' end of Norwalk virus mRNA contains determinants that regulate the expression and stability of the viral capsid protein VP1: a novel function for the VP2 protein." J Virol 77(21): 11603-15.
	Norwalk virus (NV) is the prototype strain of a group of noncultivable human caliciviruses responsible for epidemic outbreaks of acute gastroenteritis. The capsid protein VP1 is synthesized from a subgenomic RNA that contains two open reading frames (ORFs), ORF2 and ORF3, and the 3' untranslated region (UTR). ORF2 and ORF3 code for the capsid protein (VP1) and a small structural basic protein (VP2), respectively. We discovered that the yields of virus-like particles (VLPs) composed of VP1 are significantly reduced when this protein is expressed from ORF2 alone. To determine how the 3' terminus of the NV subgenomic RNA regulates VP1 expression, we compared VP1 expression levels by using recombinant baculovirus constructs containing different 3' elements. High VP1 levels were detected by using a recombinant baculovirus that contained ORF2, ORF3, and the 3'UTR (ORF2+3+3'UTR). In contrast, expression of VP1 from constructs that lacked the 3'UTR (ORF2+3), ORF3 (ORF2+3'UTR), or both (ORF2 alone) was highly reduced. Elimination of VP2 synthesis from the subgenomic RNA by mutation resulted in VP1 levels similar to those obtained with the ORF2 construct alone, suggesting a cis role for VP2 in upregulation of VP1 expression levels. Comparisons of the kinetics of RNA and capsid protein expression levels by using constructs with or without ORF3 or the 3'UTR revealed that the 3'UTR increased the levels of VP1 RNA, whereas the presence of VP2 resulted in increased levels of VP1. Furthermore, VP2 increased VP1 stability and protected VP1 from disassembly and protease degradation. The increase in VP1 expression levels caused by the presence of VP2 in cis was also observed in mammalian cells.

Bertucci, J. J., C. Lue-Hing, et al. (1977). "Inactivation of Viruses During Anaerobic Sludge Digestion." Journal - Water Pollution Control Federation 49(7): 1642-1651.
	The possibility of increased virus burden to the environment caused by land application of digested municipal sludge was a major concern of the Metropolitan Sanitary District of Greater Chicago at its Fulton County Land Reclamation site in central Illinois, USA. Viruses in wastewater are adsorbed and concentrated by sludge floc during the activated sludge process, and are carried into the anaerobic digestion process. The virus inactivation potential of the digestion process was investigated by using 5 viruses and laboratory-scale digestion units. The viruses studied included coliphage MS-2, poliovirus-1, coxsackieviruses A-9 and B-4, and echovirus-11. Average individual virus inactivation rates ranged from 74.9-97.1% after 24 h to 93.7-99.9% after 48 h.

Betts, A. O., P. H. Lamont, et al. (1962). "Porcine enteroviruses other than the virus of Teschen disease." Ann N Y Acad Sci 101: 428-35.
	
Beuret, C. (2003). "A simple method for isolation of enteric viruses (noroviruses and enteroviruses) in water." J Virol Methods 107(1): 1-8.
	A simple and improved protocol for the isolation and detection of noroviruses ('Norwalk-like viruses', NLVs) and enteroviruses in ground- and drinking water is described. An improved procedure was developed for concentration of enteric viruses from water, whereby viruses are directly lysed after filtration on a negatively charged membrane. As the method is free from possible recovery losses during usual rinsing, elution, flocculation or concentration steps prior to RNA extraction, a high sensitivity and reliability is achieved. Detection was carried out by using a modified reverse-transcription polymerase chain reaction described previously and agarose gel electrophoresis. The overall detection sensitivity of our method by spiking 1 l of water was 0.1 PFU for polioviruses (Sabine 1). For Norwalk-like viruses ggII (Lordsdale), the detection limit is clearly lower compared to older protocols with elution and concentration steps (concentration of viral particles in positive stool samples were not known). Another simple protocol was used to isolate NLVs from contaminated stool samples.

Beuret, C. (2004). "Simultaneous detection of enteric viruses by multiplex real-time RT-PCR." J Virol Methods 115(1): 1-8.
	A multiplex real-time RT-PCR protocol for the simultaneous detection of noroviruses ("Norwalk-like viruses") of genogroups I and II, human astroviruses and enteroviruses is described. The protocol was developed and evaluated using the LightCycler and corresponding SYBR Green reagents. New primers were designed within conserved genome regions to optimize the detection range of virus subtypes of each genus. To enable the development of a multiplex PCR assay within one tube (capillary), similar mastermix- and cycling-conditions were respected for each individual primer system. Subsequent melting curve analysis allowed the determination of possible dual-contaminations of entero- and noro- or astroviruses by the formation of dual peaks. Special care was taken to minimize the loss of sensitivity, since the detection of small viral contaminations is a crucial parameter especially for food analysis. The multiplex assay was compared successfully to the single SYBR Green assay, and revealed to be at least 10 times more sensitive than the one obtained with an endpoint PCR thermocycler protocol published previously.

Beuret, C., A. Baumgartner, et al. (2003). "Virus-contaminated oysters: a three-month monitoring of oysters imported to Switzerland." Appl Environ Microbiol 69(4): 2292-7.
	Molluscan shellfish are known to be carriers of viral and bacterial pathogens. The consumption of raw oysters has been repeatedly linked to outbreaks of viral gastroenteritis and hepatitis A. Switzerland imports over 300 tons of oysters per year, 95% of which originate in France. To assess the level of viral contamination, a 3-month monitoring study was conducted. Therefore, the sensitivities of several previously described methods for virus concentration were compared, and one protocol was finally chosen by using dissected digestive tissues. Eighty-seven samples consisting of five oysters each were analyzed for Norwalk-like viruses (NLVs), enteroviruses, and hepatitis A viruses from November 2001 to February 2002. The oysters were exported by 31 French, three Dutch, and two Irish suppliers. Eight oyster samples from six French suppliers were positive for NLVs, and four samples from four French suppliers were positive for enteroviruses; two of the latter samples were positive for both viral agents. No hepatitis A viruses were detected. The sequences of NLV and enterovirus amplicons showed a great variety of strains, especially for the NLVs (strains similar to Bristol, Hawaii, Mexico, and Melksham agent). The data obtained indicated that imported oysters might be a source of NLV infection in Switzerland. However, further studies are needed to determine the quantitative significance of the risk factor within the overall epidemiology of NLVs.

Beuret, C., D. Kohler, et al. (2002). "Norwalk-like virus sequences in mineral waters: one-year monitoring of three brands." Appl Environ Microbiol 68(4): 1925-31.
	In a recent study, RNA with nucleotide sequeces specific for "Norwalk-like viruses" (NLV) was detected in 11 different brands of European mineral waters. To clarify this finding, a 1-year monitoring study was conducted. Samples of three European brands of mineral water without gas were monitored weekly by reverse transcriptase PCR using generic and genogroup-specific oligonucleotides. Additional analyses were performed to investigate a possible correlation between NLV sequence contamination and mineral water lot numbers, the long-term stability (persistence) of NLV sequences in mineral water, and the level of contamination. NLV sequences were detected in 53 of 159 samples analyzed (33%) and belonged entirely to genogroup II. Although all NLV strains identified were closely related, three mineral water brand-specific clusters could be identified for both primer systems by sequencing. Analyses of second samples from lots previously shown to be positive for NLV sequences gave corresponding results in 45 of 53 cases (85%) (within a six-pack). NLV persistence was tested by analyzing 10 positive samples after 6 and 12 months of storage in darkness at room temperature. After 6 months, all samples remained positive; after 12 months, 9 of 10 samples were still positive for NLV sequences. No NLV sequences could be detected by analysis of 0.1-liter aliquots of 53 samples shown to be positive by testing of 1-liter volumes. Based on this fact and a test sensitivity of approximately 10 viral units, levels of contamination in positive mineral water samples were estimated to be in the range of 10 to 100 genomic equivalents per liter.

Beuret, C., D. Kohler, et al. (2000). "Norwalk-like virus sequences detected by reverse transcription-polymerase chain reaction in mineral waters imported into or bottled in Switzerland." J Food Prot 63(11): 1576-82.
	Norwalk-like viruses (NLVs) is a genus belonging to the Caliciviridae. NLVs are transmitted by the fecal-oral and the aerosol route and are the most common cause of outbreaks of nonbacterial gastroenteritis. NLVs are responsible for an estimated 67% of all illnesses caused by known foodborne pathogens and for 96% of nonbacterial gastroenteritis in the United States. Many outbreaks could be associated with the consumption of primarily or secondarily contaminated foods. To our knowledge, no epidemic arising from contaminated mineral water has been reported. We investigated the presence of NLV sequences in 63 mineral waters of 29 different brands that were imported into or bottled in Switzerland. NLV sequences were detected in 21 mineral waters by reverse transcription-seminested polymerase chain reaction. Specimens of two NLV genogroups (gg), gg I and gg II, were randomly present in the contaminated samples. The presence of NLV sequences could not be correlated either with bottle characteristics or with chemical properties like mineralization, pH, or the presence of carbonic acid. Nucleotide sequence analysis of 12 NLV-positive samples revealed several point mutations. All isolated NLV gg I strains have a similarity of 70 to 87% with the common Desert Shield virus (UO4469), and all isolated NLV gg II strains have a similarity of 89 to 93% with the Camberwell virus (U46500). Possible reasons for the presence of NLV sequences in mineral waters are discussed.

Bhattacharji, L. M., A. L. Saha, et al. (1963). "Investigation of an outbreak of infectious hepatitis in a small town in West Bengal during July-October, 1960." Indian Journal of Medical Research 51: 550-562.
	
Bhattacharya, S. S., M. Kulka, et al. (2004). "Use of reverse transcription and PCR to discriminate between infectious and non-infectious hepatitis A virus." J Virol Methods 116(2): 181-7.
	Hepatitis A virus (HAV) is a major cause of infectious hepatitis worldwide. Detection of HAV in contaminated food or water is a priority research area in laboratories worldwide. Our laboratory has reported previously the development of reverse transcription-polymerase chain reaction (RT-PCR) based detection and typing methods for HAV in contaminated shellfish and produce. It is commonly held that RT-PCR can detect viral genome, but cannot distinguish between infectious and inactivated virus. Therefore, signals obtained after PCR should be considered as false positives unless it can be shown that the sample contains virus capable of infecting a suitable host cell line in culture. We present data to show that this general assumption is not valid. Evidence is provided that demonstrate that signals generated after RT-PCR amplification of viral genome correlated well with the presence of infectious virus in the sample. Viral samples inactivated by heat or UV treatment produced significantly lower signal strength that paralleled infectivity of the sample in cultured cells. The loss of signal strength is most likely the result of damage to the viral RNA that renders it unsuitable for RT-PCR. The correlation between PCR signal and infectivity was better following UV inactivation than heat treatment. The procedure may be adapted to other viruses and inactivating agents.

Biagini, P., P. Gallian, et al. (2001). "Comparison of systems performance for TT virus detection using PCR primer sets located in non-coding and coding regions of the viral genome." J Clin Virol 22(1): 91-9.
	BACKGROUND: the heterogeneity of the TT virus (TTV) DNA prevalence values reported from comparable human cohorts suggests that diagnostic PCR protocols still require to be optimized. OBJECTIVES: to design TTV PCR primer sets with low genotype restriction and to compare their performances with commonly used amplification systems. STUDY DESIGN: we compared full length TTV genomic sequences and identified conserved nucleotide patterns in the 5' and 3' non-coding regions of the viral genome. This permitted to design two new primer sets usable for the PCR amplification of the most divergent human isolates of TTV described to date. The performances of these amplification systems were compared with those of three other PCR systems earlier used for prevalence studies. RESULTS: the primer systems P5Bx and P3Bx exhibited higher PCR scores than the other systems tested; 14 to 34% improvement values were obtained, and divergent positive results of earlier described PCR systems were confirmed systematically by our new detection assays. CONCLUSIONS: an optimized detection of TT virus DNA is a pre-requisite for the accurate epidemiological survey of viral infection and for the realization of phylogenetic studies. Such PCR systems with low genotype restriction will be helpful in the future for a better knowledge of natural history of TT virus infection.

Bidawid, S., J. M. Farber, et al. (2000). "Contamination of foods by food handlers: experiments on hepatitis A virus transfer to food and its interruption." Appl. Environ. Microbiol. 66(7): 2759-2763.
	Hepatitis A virus (HAV) is an important pathogen which has been responsible for many food-borne outbreaks. HAV-excreting food handlers, especially those with poor hygienic practices, can contaminate the foods which they handle. Consumption of such foods without further processing has been known to result in cases of infectious hepatitis. Since quantitative data on virus transfer during contact of hands with foods is not available, we investigated the transfer of HAV from artificially contaminated fingerpads of adult volunteers to pieces of fresh lettuce. Touching the lettuce with artificially contaminated fingerpads for 10 s at a pressure of 0.2 to 0.4 kg/cm(2) resulted in transfer of 9.2% +/- 0.9% of the infectious virus. The pretreatments tested to interrupt virus transfer from contaminated fingerpads included (i) hard-water rinsing and towel drying, (ii) application of a domestic or commercial topical agent followed by water rinsing and towel drying, and (iii) exposure to a hand gel containing 62% ethanol or 75% liquid ethanol without water rinsing or towel drying. When the fingerpads were treated with the topical agents or alcohol before the lettuce was touched, the amount of infectious virus transferred to lettuce was reduced from 9.2% to between 0.3 and 0.6% (depending on the topical agent used), which was a reduction in virus transfer of up to 30-fold. Surprisingly, no virus transfer to lettuce was detected when the fingerpads were rinsed with water alone before the lettuce was touched. However, additional experiments with water rinsing in which smaller volumes of water were used (1 ml instead of 15 ml) showed that the rate of virus transfer to lettuce was 0.3% +/- 0.1%. The variability in virus transfer rates following water rinsing may indicate that the volume of water at least in part influences virus removal from the fingerpads differently, a possibility which should be investigated further. This study provided novel information concerning the rate of virus transfer to foods and a model for investigating the transfer of viral and other food-borne pathogens from contaminated hands to foods, as well as techniques for interrupting such transfer to improve food safety.

Bidawid, S., J. M. Farber, et al. (2000). "Contamination of foods by food handlers: experiments on hepatitis A virus transfer to food and its interruption." Appl Environ Microbiol 66(7): 2759-63.
	Hepatitis A virus (HAV) is an important pathogen which has been responsible for many food-borne outbreaks. HAV-excreting food handlers, especially those with poor hygienic practices, can contaminate the foods which they handle. Consumption of such foods without further processing has been known to result in cases of infectious hepatitis. Since quantitative data on virus transfer during contact of hands with foods is not available, we investigated the transfer of HAV from artificially contaminated fingerpads of adult volunteers to pieces of fresh lettuce. Touching the lettuce with artificially contaminated fingerpads for 10 s at a pressure of 0.2 to 0.4 kg/cm(2) resulted in transfer of 9.2% +/- 0.9% of the infectious virus. The pretreatments tested to interrupt virus transfer from contaminated fingerpads included (i) hard-water rinsing and towel drying, (ii) application of a domestic or commercial topical agent followed by water rinsing and towel drying, and (iii) exposure to a hand gel containing 62% ethanol or 75% liquid ethanol without water rinsing or towel drying. When the fingerpads were treated with the topical agents or alcohol before the lettuce was touched, the amount of infectious virus transferred to lettuce was reduced from 9.2% to between 0.3 and 0.6% (depending on the topical agent used), which was a reduction in virus transfer of up to 30-fold. Surprisingly, no virus transfer to lettuce was detected when the fingerpads were rinsed with water alone before the lettuce was touched. However, additional experiments with water rinsing in which smaller volumes of water were used (1 ml instead of 15 ml) showed that the rate of virus transfer to lettuce was 0.3% +/- 0.1%. The variability in virus transfer rates following water rinsing may indicate that the volume of water at least in part influences virus removal from the fingerpads differently, a possibility which should be investigated further. This study provided novel information concerning the rate of virus transfer to foods and a model for investigating the transfer of viral and other food-borne pathogens from contaminated hands to foods, as well as techniques for interrupting such transfer to improve food safety.

Bidawid, S., J. M. Farber, et al. (2000). "Inactivation of hepatitis A virus (HAV) in fruits and vegetables by gamma irradiation,." Int. J. Food Microbiol. 57: 91-97.
	
Bidawid, S., J. M. Farber, et al. (2000). "Rapid concentration and detection of hepatitis A virus from lettuce and strawberries." J Virol Methods 88(2): 175-85.
	Immunomagnetic beads-PCR (IM-PCR), positively-charged virosorb filters (F), or a combination of both methods (F-IM-PCR) were used to capture, concentrate and rapidly detect hepatitis A virus (HAV) in samples of lettuce and strawberries experimentally contaminated. Direct reverse transcriptase-polymerase chain reaction (RT-PCR) amplification of the collected HAV-beads complex showed a detection limit of 0.5 plaque forming units (PFU) of the virus present in 1-ml of wash solution from the produce, which was several hundred-fold more sensitive than that demonstrated by RT-PCR. In separate trials, virus-containing wash solutions from the produce were passed through the filters and the captured virus was eluted with 10 ml volumes of 1% beef extract. Of the 62% filter-captured HAV, an average of 34.8% was eluted by the 1% beef extract. PCR amplification of 2 microl from this eluate failed to produce a clear positive band signal. As little as 10 PFU, present on each piece of the lettuce or strawberry, was detectable by the F-IM-PCR, which was almost 20 times less sensitive than the detection limit of 0.5 PFU by the IM-PCR. However, considering the large volumes (< or =50 ml) used in the F-IM-PCR, the sensitivity of detection could be much greater than that of the IM-PCR, which was restricted to < or =20 ml volumes. These data indicate that the F-IM-PCR method provides the potential for a greater sensitivity of detection than the IM-PCR, since low levels of virus could be detected from large volumes of sample than possible by the IM-PCR method. Although positively-charged filters captured a greater amount of virus than both the IM-PCR and F-IM-PCR methods, direct PCR amplification from beef extract eluates was not successful in detecting HAV from produce.

Bidawid, S., J. M. Farber, et al. (2001). "Survival of hepatitis A virus on modified atmosphere-packaged (MAP) lettuce." Food Microbiology 18(1): 95-102.
	Experiments were designed to study the effect of various modified atmospheres (MA) on the survival rate of hepatitis A virus (HAV) on lettuce. Pieces of lettuce inoculated with HAV were incubated at room temperature (RT) and 4 degree C for 12 days in ambient air and under various modified atmospheres (CO sub(2):N sub(2)at 30:70, 50:50, 70:30 and 100% CO sub(2)) inside plastic bags of low O sub(2)permeability. Samples were removed on days 1, 3, 6, 9 and 12 and the virus was recovered and plaque-assayed to determine residual titer. Incubation for 12 days at 4 degree C showed that the lowest HAV survival rate (47.5%) was on lettuce stored in a petri-dish (atmospheric air), whereas the greatest survival rates (83.6%) was on lettuce stored under 70% CO sub(2). Statistical analysis of virus survival at 4 degree C indicated that HAV titers decreased for all packages, but without a significant (P>0.05) difference between the package types. At RT, however, a significantly (P<0.05) lower HAV survival rate (0.01%) was evident on lettuce stored in a petri dish, whereas survival rates as high as 42.8% were observed on lettuce stored under 70% CO sub(2); much lower survival rates ( less than or equal to 8.6%) were obtained on lettuce stored under other MAP environments at RT. Statistical analysis of the RT data indicated that there was a highly significant (P<0.05) decrease in HAV titre with increasing storage time and between package types, except for lettuce stored under 70% CO sub(2). These data indicate that MAP does not influence HAV survival when present on the surface of produce incubated at 4 degree C. A slight improvement in virus survival on lettuce was seen in the presence of high CO sub(2)levels at RT. This may have been attributed to the inhibition of spoilage-causing enzymatic activities in the lettuce, which may have reduced exposure of the virus to potential toxic by-products. Copyright 2001 Academic Press.

Bidawid, S., J. M. Farber, et al. (2000). "Heat inactivation of hepatitis A virus in dairy foods." J. Food Prot. 63(4): 522-528.
	Experiments were performed to determine the thermal resistance of hepatitis A virus (HAV) in three types of dairy products containing increased amounts of fat content (skim milk, homogenized milk; 3.5% MFG, and table cream; 18% MFG). HAV-inoculated dairy products were introduced into custom-made U-shaped microcapillary tubes that in turn were simultaneously immersed in a waterbath, using custom-made floating boats and a carrying platform. Following exposure to the desired time and temperature combinations, the contents of each of the tubes was retrieved and was tested by plaque assay to determine the reduction in virus titer. Our data indicated that < 0.5 min at 85 degrees C was sufficient to cause a 5-log reduction in HAV titer in all three dairy products, whereas at 80 degrees C, < or = 0.68 min (for skim and homogenized milk), and 1.24 min (for cream) were needed to cause a similar log reduction. Using a nonlinear two-phase negative exponential model (two-compartment model) to analyze the data, it was found that at temperatures of 65, 67, 69, 71, and 75 degrees C, significantly (P < 0.05) higher exposure times were needed to achieve a 1-log reduction in virus titer in cream, as compared to skim and homogenized milk. For example, at 71 degrees C, a significantly (P < 0.05) higher exposure time of 0.52 min (for cream) was needed as compared to < or = 0.18 min (for skim and homogenized milk) to achieve a 1-log reduction in virus titer. A similar trend of inactivation was observed at 73 and 75 degrees C where significantly (P < 0.05) higher exposure times of 0.29 to 0.36 min for cream were needed to cause a 1-log reduction in HAV in cream, as compared to < or = 0.17 min for skim and homogenized milk. This study has provided information on the heat resistance of HAV in skim milk, homogenized milk, and table cream and demonstrated that an increase in fat content appears to play a protective role and contributes to the heat stability of HAV.

Bidawid, S., N. Malik, et al. (2003). "A feline kidney cell line-based plaque assay for feline calicivirus, a surrogate for Norwalk virus." J Virol Methods 107(2): 163-7.
	Feline calicivirus (FCV) has been used by researchers as a surrogate for Norwalk virus (NV), since they share a similar genomic organization, physicochemical characteristics, and are grouped in the same family, Caliciviridae. Unlike NV, however, FCV can grow in established cell lines and produce a syncytial form of cytopathic effect. In this report, we describe the development and standardization of a plaque assay for FCV using monolayers of an established line of feline kidney (CrFK) cells in 12-well cell culture plates. The assay method has demonstrated reproducibility, ease of performance and resulted in clear plaque zones, readable in 24 h after virus inoculation. The infectivity titre of the virus by this plaque assay agreed well with tissue culture infectious dose(50) (TCID(50)) determinations. The described plaque assay would be a valuable tool in conducting various quantitative investigations using FCV as a model for NV and Norwalk-like viruses (NLV).

Bidawid, S., N. Malik, et al. (2004). "Norovirus cross-contamination during food handling and interruption of virus transfer by hand antisepsis: experiments with feline calicivirus as a surrogate." J Food Prot 67(1): 103-9.
	While there is good epidemiological evidence for foods as vehicles for norovirus transmission, the precise means of spread and its control remain unknown. The feline calicivirus was used as a surrogate for noroviruses to study infectious virus transfer between hands and selected types of foods and environmental surfaces. Assessment of the potential of selected topicals in interrupting such virus transfer was also made. Ten microliters of inoculum of feline calicivirus deposited onto each fingerpad of adult subjects was allowed to air dry and the contaminated area on individual fingerpads was pressed (10 s at a pressure of 0.2 to 0.4 kg/cm2) onto 1-cm-diameter disks of ham, lettuce, or brushed stainless steel. The virus remaining on the donor and that transferred to the recipient surfaces was eluted and plaque assayed. Virus transfer to clean hands from experimentally contaminated disks of ham, lettuce, and stainless steel was also tested. Nearly 46 +/- 20.3, 18 +/- 5.7, and 13 +/- 3.6% of infectious virus was transferred from contaminated fingerpads to ham, lettuce, and metal disks, respectively. In contrast, approximately 6 +/- 1.8, 14 +/- 3.5, and 7 +/- 1.9% virus transfer occurred, respectively, from ham, lettuce, and metal disks to hands. One-way analysis of variance test showed that pretreatment (washing) of the fingerpads either with water or with both topical agent and water significantly (P < 0.05) reduced virus transfer to < or = 0.9%, as compared with < or = 2.3 and < or = 3.4% transfer following treatments with either 75% (vol/vol) ethanol or a commercial hand gel containing 62% ethanol, respectively. Despite wide variations in virus transfer among the targeted items used, intervention agents tested reduced virus transfer significantly (P < 0.05) when compared with that without such treatments (71 +/- 8.9%). These findings should help in a better assessment of the potential for cross-contamination of foods during handling and also assist in developing more effective approaches to foodborne spread of norovirus infections.

Bienz, K., D. Egger, et al. (1992). "Structural and functional characterization of the poliovirus replication complex." J Virol 66(5): 2740-7.
	Two populations of membrane-bound replication complexes were isolated from poliovirus-infected HEp-2 cells by sucrose gradient centrifugation. The two fractions show similar ultrastructural features: the replication complex is enclosed in a rosettelike shell of virus-induced vesicles and contains a very tightly packed second membrane system (compact membranes). The vesicular fraction, which bands in 30% sucrose, contains replicative intermediate (RI) and 36S RNA. The fraction banding in 45% sucrose contains only minute amounts of RI and contains mainly 36S RNA, two-thirds of which is encapsidated. In vitro, the two fractions show similar RNA synthesizing capacities and produce 36S plus-strand RNA. Dissolving the membranes within and around synthetically active replication complexes with sodium deoxycholate abolishes the completion of 36S RNA but still allows elongation in the RI. Our findings suggest an architecture of the replication complex that has the nascent plus strands on the RI enclosed in the compact membranes and the replication forks wrapped additionally in protein. Plus-strand RNA can be localized by in situ hybridization with a biotinylated riboprobe between the replication complex and the rosette of the virus-induced vesicles. It was found that the progeny RNA strands are set free soon after completion from the replication complex at the sites where the compact membranes within the replication complex are in close contact with the surrounding virus-induced vesicles.

Bieschke, J., A. Giese, et al. (2000). "Ultrasensitive detection of pathological prion protein aggregates by dual-color scanning for intensely fluorescent targets." Proc Natl Acad Sci U S A 97(10): 5468-73.
	A definite diagnosis of prion diseases such as Creutzfeldt-Jakob disease (CJD) relies on the detection of pathological prion protein (PrP(Sc)). However, no test for PrP(Sc) in cerebrospinal fluid (CSF) has been available thus far. Based on a setup for confocal dual-color fluorescence correlation spectroscopy, a technique suitable for single molecule detection, we developed a highly sensitive detection method for PrP(Sc). Pathological prion protein aggregates were labeled by specific antibody probes tagged with fluorescent dyes, resulting in intensely fluorescent targets, which were measured by dual-color fluorescence intensity distribution analysis in a confocal scanning setup. In a diagnostic model system, PrP(Sc) aggregates were detected down to a concentration of 2 pM PrP(Sc), corresponding to an aggregate concentration of approximately 2 fM, which was more than one order of magnitude more sensitive than Western blot analysis. A PrP(Sc)-specific signal could also be detected in a number of CSF samples from patients with CJD but not in control samples, providing the basis for a rapid and specific test for CJD and other prion diseases. Furthermore, this method could be adapted to the sensitive detection of other disease-associated amyloid aggregates such as in Alzheimer's disease.

Biffiger, K., D. Zwald, et al. (2002). "Validation of a luminescence immunoassay for the detection of PrP(Sc) in brain homogenate." J Virol Methods 101(1-2): 79-84.
	A luminescence immunoassay (LIA) was developed for the diagnosis of bovine spongiform encephalopathy (BSE) in brain tissue using two different monoclonal antibodies for capture and detection of the protease-resistant fragment of the pathological prion protein (PrP27-30). PrP27-30 currently represents the most reliable marker for the infectious particle (denominated prion) causing transmissible spongiform encephalopathies (TSEs). Internal and official validation studies of this assay are described using brain homogenates from ascertained BSE positive and negative cows. Using more than 300 positive and 1400 negative bovine or ovine samples, an excellent sensitivity and specificity of 100% were demonstrated. More than 1000-fold dilutions of a BSE positive homogenate still resulted in a clear positive signal. In combination with a simple homogenisation procedure for the preparation of the samples, this assay lends itself for large scale screening of cattle and sheep for TSEs using complete automation of the process.

Bile, K., A. Isse, et al. (1994). "Contrasting roles of rivers and wells as sources of drinking water on attack and fatality rates in a hepatitis E epidemic in Somalia." American Journal of Tropical Medicine and Hygiene 51(4): 466-474.
	In early 1988, an increased incidence of acute hepatitis was observed in villages along the Shebeli River in the Lower Shebeli region of Somalia. This was followed by a large epidemic that lasted until late 1989. In a survey of 142 villages with a population of 245,312 individuals, 11,413 icteric cases were recorded, of which 346 died, corresponding to an attack rate and a case fatality rate of 4.6% and 3.0%, respectively. The etiologic role of hepatitis E virus (HEV) in this epidemic was proven by demonstrating anti-HEV in 128 of 145 sampled cases as a sign of recent infection with HEV. In three villages, where a special study protocol was implemented, the attack rate was found to increase significantly with age from 5% in the group 1-4 years of age to 13% in the group 5-15 years of age and to 20% for persons older than 15 years of age. Among cases 20-39 years of age, the female-to-male ratio was 1.5:1, which was a significant predominance of females. As in other hepatitis E outbreaks, there was a high fatality rate in pregnant females, estimated to be 13.8%. The epidemic peaked with the rise in the level of the river during rainfall, suggesting that the disease was waterborne. The attack rate was higher (6.0%) in villages supplied with river water, while fewer cases were recorded in those relying on wells or ponds for their water supply, 1.7% and 1.2%, respectively. 

Billgren, M., B. Christenson, et al. (2002). "Epidemiology of Norwalk-like Human Caliciviruses in Hospital Outbreaks of Acute Gastroenteritis in the Stockholm Area in 1996." J Infect 44(1): 26-32.
	Objectives: Outbreaks of acute gastroenteritis associated with 'Norwalk-like viruses' (NLVs) cause significant health problems in hospitals. Hospital outbreaks in the Stockholm area in 1996 were investigated, in order to identify the magnitude of the problem, the mode of transmission, the effect of control measures and the genetic variability of outbreak strains. Determining the epidemiological and clinical significance involves a broad range of possibilities.Methods: Ten hospitals, representing 66% of the hospitals in the Stockholm area, participated in the study, which included 211 wards. Of these, 18 were selected as control. A standardized protocol that included personal contacts was administered. Outbreak wards were visited between 5 and 10 times. Wards that had reported outbreaks in 1996 were prospectively followed through 1999 by personal contacts, and the available data from 1991 on outbreak reports were collected. A total of 253 stool samples from outbreaks in 1996 were analyzed by electron microscopy (EM) for the presence of NLVs. Positive samples were confirmed by the reverse transcriptase-polymerase chain reaction (RT-PCR).Results: In total, 4 326 patients and 1 119 staff were exposed on the 43 wards that reported 54 outbreaks. The mean attack rate was 13% for patients and 21% for staff. The number of outbreaks in 1996 outnumbered the reported outbreaks in the preceding years (4-70%) and later years (35-40%). Admission to 24 (56%) of the outbreak wards was stopped. The mean duration of illness for patients was 35 hours and for staff, 30 hours. The main symptoms were diarrhoea (80%) and vomiting (68%). Genotyping revealed that the majority of the hospital outbreaks in the Stockholm area in 1996 were caused by a single NLV strain.Conclusions: The study confirmed that outbreaks of NLV are an increasing public-health problem in hospitals. The risk of being affected by an outbreak was significantly greater on wards that had reported outbreaks in the previous year. It was not obvious which measures had helped to shorten the outbreaks to any appreciable extent. Different managements must therefore be carefully interpreted and adapted to the prevailing circumstances. Genotyping of strains is an important tool of getting a better insight into transmission routes and the mechanism behind the appearance of epidemic strains.

Binn, L. N., S. M. Lemon, et al. (1984). "Primary isolation and serial passage of hepatitis A virus strains in primate cell cultures." Journal of Clinical Microbiology 20(1): 28-33.
	Although several primate cell types have been reported to support replication of hepatitis A virus, optimal conditions for the isolation and production of quantities of virus have not been defined. We therefore examined seven different primate cell types for their ability to support replication of primate-passaged and wild-type virus as reflected by intracytoplasmic accumulation of viral antigen (direct immunofluorescence and radioimmunoassay) and propagation of cell culture-adapted virus. Of the cells tested, low-passage African green monkey kidney (AGMK) cells were most sensitive for initial isolation. Viral replication was documented after inoculation of AGMK cells with seven of nine hepatitis A virus antigen-positive fecal specimens (from seven epidemiologically distinct sources). With six inocula, virus was successfully passed in serial cultures. AGMK-adapted virus was readily propagated in continuous AGMK (BS-C-1) cells. The optimal temperature for the growth of virus in BS-C-1 cells was 35 degrees C. Viral release into supernatant fluids was documented in the absence of any cytopathic effect, and infectivity titers in supernatant fluids 21 days after inoculation (50% tissue culture infective does [TCID50], 10(6.0)/ml) equalled or exceeded those in the cell fraction (TCID50, 10(5.5)/ml). Cells maintained in serum-free media readily supported viral growth, with yields of virus (TCID50, 10(6.5)/ml) equal to or greater than those obtained with cells maintained in 2% fetal bovine serum.

Birch, C. J., S. M. Rodger, et al. (1983). "Replication of human rotavirus in cell culture." J Med Virol 11(3): 241-50.
	Nine strains of human rotavirus were adapted to growth in CV-1 and/or MA-104 cells following pretreatment of virus with trypsin, incorporation of trypsin into culture medium, and use of roller cultures. Immunofluorescence was the most reliable method for the detection of virus replication, although characteristic cytopathic effects were produced sporadically by most isolates. Virus could be readily detected in supernatant fluids of cell cultures and in cell sections by electron microscopy.

Birkenmeyer, L. G. and I. K. Mushahwar (1994). "Detection of hepatitis A, B, and D virus by the polymerase chain reaction." Journal of Virological Methods 49(2): 101-112.
	Mini-Review

Bishop, N. and D. Anderson (1997). "Early interaction of hepatitis A virus with cultured cells: viral elution and the effect of pH and calcium ions." Archives of Virology 142: 2161-2178.
	
Bishop, N. E. and D. A. Anderson (1993). "RNA-dependent cleavage of VP0 capsid protein in provirions of hepatitis A virus." Virology 197(2): 616-23.
	Stable provirions of hepatitis A virus containing up to 62% VP0 were purified from infected BS-C-1 cells by sucrose density gradient ultracentrifugation, and conversion of these provirions to virions through maturation cleavage of VP0 capsid protein was demonstrated. VP0 cleavage was slow but linear over 7 days at 37 degrees, with mature virions containing between 3 and 7 copies of VP0 in separate experiments. Cleavage of approximately 25% of VP0 molecules (15 copies) was accompanied by a twofold increase in specific infectivity. Particles with reduced levels of VP0 were observed to sediment more rapidly in sucrose than VP0-rich provirions, reflecting conformational changes in the particles. The kinetics and temperature-dependence of VP0 cleavage further suggest that such conformational changes accompanying VP0 cleavage are necessary for the formation of subsequent catalytic sites.

Bishop, N. E., D. L. Hugo, et al. (1994). "Rapid and efficient purification of hepatitis A virus from cell culture." Journal of Virological Methods 47(1-2): 203-216.
	Hepatitis A virus (HAV) characteristically remains strongly cell-associated when grown in culture, with only small yields in the culture supernatant. Cell factories (6000 cm2) of BS-C-1 cells infected with the cytopathic HM175A.Z strain of HAV for 3, 4 or 7 days were harvested using trypsin to disperse the infected cell monolayer, and cells were collected by low speed centrifugation. More than 70% of the yield of virus and viral antigen can thus be obtained in the packed cell pellet. Packed cell pellets were resuspended in 5 volumes of isotonic buffer and cell membranes lysed by the addition of a non-ionic detergent. After removal of nuclei by centrifugation, ionic detergent was added to the clarified cytoplasmic extract. Under these conditions, HAV particles (virions and empty capsids) are the only particulate material remaining in the sample, and were recovered in a single ultracentrifugation step through discontinuous sucrose/glycerol density gradients. In one day, this method yields viral antigen with minimal cellular contaminants, in a concentrated volume suitable for subsequent biochemical, vaccine or diagnostic uses. The yield of viral antigen over numerous batches varied from 200 to 1600 vaccine-equivalent doses per cell factory, with a titre of up to 1 x 10(10) infectious particles per ml. 

Bishop, R. F., G. P. Davidson, et al. (1973). "Letter: Evidence for viral gastroenteritis." N Engl J Med 289(20): 1096-7.
	
Bishop, R. F., G. P. Davidson, et al. (1973). "Virus particles in epithelial cells of duodenal mucosa from children with acute non-bacterial gastroenteritis." Lancet 2(7841): 1281-3.
	
Bishop, R. F., G. P. Davidson, et al. (1974). "Detection of a new virus by electron microscopy of faecal extracts from children with acute gastroenteritis." Lancet 1(7849): 149-51.
	
Bishop, R. F., P. J. Masendycz, et al. (2001). "Epidemiological patterns of rotaviruses causing severe gastroenteritis in young children throughout Australia from 1993 to 1996." J Clin Microbiol 39(3): 1085-91.
	Rotavirus strains that caused severe diarrhea in 4,634 (2,533 male) children aged less than 5 years and admitted to major hospitals in eight centers throughout Australia from 1993 to 1996 were subject to antigenic and genetic analyses. The G serotypes of rotaviruses were identified in 81.9% (3,793 of 4,634) children. They included 67.8% (from 3,143 children) serotype G1 isolates (containing 46 electropherotypes), 11.5% (from 531 children) serotype G2 isolates (27 electropherotypes), 0.8% (from 39 children) serotype G3 isolates (8 electropherotypes), and 1.6% (from 76 children) serotype G4 isolates (9 electropherotypes). G6 (two strains) and G8 (two strains) isolates were identified during the same period. G1 serotypes were predominant in all centers, with intermittent epidemics of G2 serotypes and sporadic detection of G3 and G4 strains. With the exception of two strains (typed as G1P2A[6] and G2P2A[6]) all serotype G1, G3, and G4 strains were P1A[8] and all serotype G2 strains were P1B[4]. Two contrasting epidemiological patterns were identified. In all temperate climates rotavirus incidence peaked during the colder months. The genetic complexity of strains (as judged by electropherotype) was greatest in centers with large populations. Identical electropherotypes appeared each winter in more than one center, apparently indicating the spread of some strains both from west to east and from east to west. Centers caring for children in small aboriginal communities showed unpredictable rotavirus peaks unrelated to climate, with widespread dissemination of a few rotavirus strains over distances of more than 1,000 km. Data from continued comprehensive etiological studies of genetic and antigenic variations in rotaviruses that cause severe disease in young children will serve as baseline data for the study of the effect of vaccination on the incidence of severe rotavirus disease and on the emergence of new strains.

Bitton, G., L. T. Chang, et al. (1981). "Recovery of coliphages from wastewater effluents and polluted lake water by the magnetite-organic flocculation method." Appl Environ Microbiol 41(1): 93-6.
	A magnetite-organic flocculation method was developed for the concentration of coliphages from wastewater effluents and polluted lake water. A high percent (68 to 100%) recovery of coliphages from sewage effluents was achieved by this procedure. Coliphage recovery from Lake Alice, a sewage-contaminated lake, showed phage concentrations ranging from 2.3 X 10(2) to 1.9 X 10(3) plaque-forming units per liter. This method is simple and inexpensive and may be carried out under field conditions.

Bitton, G., J. M. Davidson, et al. (1979). "On the Value of Soil Columns for Assessing the Transport Pattern of Viruses Through Soils: A Critical Outlook." Water: Air, and Soil Pollution Vol 12, No 4, p 449-457.
	The U.S. Water Pollution Control Act Amendment of 1972 (PL 92-500) has made land disposal of wastewater effluents and residuals a viable and attractive alternative. Land spreading of wastewater effluents and residuals has many advantages, including the addition of plant nutrients, water conservation, improvement of soil physical properties, and increased soil organic matter. Public health risks associated with land disposal of wastes containing human pathogens can be assessed only through a thorough examination of the survival and transport pattern of these pathogens through soils. This topic has been thoroughly covered in recent reviews. In this review, the authors were primarily concerned with a critical examination of the various methods frequently used to assess soils ' potential to retain viruses. Knowledge concerning the transport pattern of viruses through soils can be gained through field monitoring of these infectious particles in wastewater effluents , sludges, soils and groundwater, and/or through soil column experiments. The latter have been criticized, and our purpose was to examine these criticisms and suggest, if necessary, some alternate solutions. Furthermore, the authors reviewed the practical information gained through soil column studies and examined, with the aid of examples of land application sites across the country, the relationship between laboratory and field studies. (Sims-ISWS)

Bitton, G., O. C. Pancorbo, et al. (1984). "Virus transport and survival after land application of sewage sludge." Appl Environ Microbiol 47(5): 905-9.
	The survival and transport patterns of poliovirus 1 and echovirus 1 were studied in undisturbed soil cores which were treated with digested sludge and exposed to natural weather conditions prevailing in north central Florida. It was shown that, under those experimental conditions, enteroviruses are relatively rapidly inactivated in the soil. A more rapid virus decline was observed during the warm and dry fall season than during the warm and wet summer season. The monitoring of soil core leachates has shown that both viruses were effectively retained by the sludge-treated soil.

Bixby, R. L. and D. J. O'Brien (1979). "Influence of fulvic acid on bacteriophage adsorption and complexation in soil." Appl Environ Microbiol 38(5): 840-5.
	The effect of fulvic acid, the major fraction of natural soluble organic matter, on the adsorption of MS2 bacteriophage to soil was investigated in controlled laboratory experiments. Batch experiments together with scanning electron microscopy-energy-dispersive X-ray analysis showed that fulvic acid complexed phage, which prevented its adsorption to soil. Phage strongly adsorbed to soil in the absence of fulvic acid. Phage which was complexed with fulvic acid was not irreversibly inactivated and could become viable under proper conditions, illustrating the importance of assay and elution procedures in the recovery of virus from aqueous solutions.

Biziagos, E., J. M. Crance, et al. (1990). "Extraction of hepatitis A virus from experimentally contaminated shellfish." Travaux Scientifiques des Chercheurs du Service de Sante des Armees(11): 47-48.
	An extraction method to recover hepatitis A virus from experimentally contaminated oysters was developed and evaluated. 80% of HAV was recovered by this method. We propose to apply it to the systematic detection of HAV in environment.

Biziagos, E., J. Passagot, et al. (1987). "Concentration of hepatitis A virus." Water Research 21(6): 683-686.
	Cell culture adapted hepatitis A virus (HAV) in 10 and 50 l. of seeded distilled water was respectively concentrated approx. 3300 and 17,000 fold by adsorption-elution on cellulose membrane. HAV (strain CF 53) was adsorbed at pH 4.0 with 0.15 M NaCl to the cellulose filters and eluted by 3% beef-extract at pH 8.5. Eluted virus was further concentrated by precipitation by polyethylene glycol 6000. Hepatitis A antigen (HAAg) was detected by radioimmunoassay and infectious virus was quantified by cell culture titration. The average of HAAg recovery was 76% for 10 l. and 85% for 50 l., whereas the average recovery for infectious virus was respectively 89 and 97%. The sensitivity of the method was tested by contaminating 10 l. with 16 TCID50 only; 63% of initial infectious virus were recovered.

Biziagos, E., J. Passagot, et al. (1988). "Long-term survival of hepatitis A virus and poliovirus type 1 in mineral water." Applied and Environmental Microbiology 54(11): 2705-2710.
	The survival in mineral water of hepatitis A virus (HAV) and poliovirus type 1 was compared, under controlled experimental conditions, at 4 degrees C and room temperature. Viral infectivity titers were determined by cell culture titration, while HAV antigenicity was monitored by radioimmunoassay-endpoint titration. Both viruses persisted longest at 4 degrees C. At this temperature, after 1 year of exposure, the inactivation of either HAV or poliovirus type 1 was not important. At room temperature, poliovirus type 1 was not detected after 300 days, whereas HAV was still infectious. For both temperatures, the computed regression coefficients of best-fit lines for inactivation rates for the two viruses were significantly different. The survival of HAV was also studied at 4 degrees C and room temperature in mineral water with 5- and 50-micrograms/ml protein concentrations (i.e., purity of the virus suspension) for 120 days. As shown by a comparison of the regression coefficients for the inactivation rates, the stability of HAV in mineral water depends on protein concentration and temperature. Radioimmunoassay-endpoint titration results showed inactivation patterns similar to those of cell culture titration, with the most significant reduction in HAV antigenicity at room temperature. At the two temperatures, the infectivity of HAV declined at a faster rate than the antigenicity. 

Biziagos, E., J. Passagot, et al. (1989). "Hepatitis A Virus Concentration from Experimentally Contaminated Distilled Tap Waste and Seawater." Water Science and Technology 21(3): 255-258.
	
Biziagos, E., M. Pons, et al. (1988). "Hepatitis A virus concentration from experimentally contaminated waters." Travaux Scientifiques des Chercheurs du Service de Sante des Armees(9): 75-76.
	An adsorption elution method on cellulose membranes followed by a PEG precipitation was used to concentrate Hepatitis A virus from experimentally contamined waters. Efficiency of recovery evaluated by HA antigen titer determination was 80% after treatment of 10 and 50 liters of tap water and 70% after use of 1 or 3 litres of wastewater.

Black, E. K. and G. R. Finch (1994). "Detection and occurrence of  waterborne bacterial and viral pathogens." Water Environment  Research 66(4): 292-298.
	
Black, R. E., H. B. Greenberg, et al. (1982). "Acquisition of serum antibody to Norwalk Virus and rotavirus and relation to diarrhea in a longitudinal study of young children in rural Bangladesh." J Infect Dis 145(4): 483-9.
	Serum antibodies to Norwalk virus and to rotavirus were measured during longitudinal studies of infectious diseases and nutrition in rural Bangladesh. Initially, the prevalence of antibody to Norwalk virus was 7% in children younger than six months and increased to 80% in children two to five years of age. The incidence of titer increases was highest in one- and two-year-olds and in children who had low or undetectable levels of antibody. Some Norwalk virus infections appeared to result in diarrhea. Nearly all children had serum antibodies to rotavirus at the beginning of the study; however, children with the lowest levels of antibody to rotavirus had the greatest risk of rotavirus diarrhea. Over half of the children had a fourfold increase in titer of antibody to rotavirus during the year, and 7% had increases in two of the three study periods during the year. Most increases in titer of antibody to rotavirus appeared to result from subclinical infections.

Blackburn, B. G., G. F. Craun, et al. (2004). "Surveillance for waterborne-disease outbreaks associated with drinking water--United States, 2001-2002." MMWR Surveill Summ 53(8): 23-45.
	PROBLEM/CONDITION: Since 1971, CDC, the U.S. Environmental Protection Agency, and the Council of State and Territorial Epidemiologists have maintained a collaborative surveillance system for collecting and periodically reporting data related to occurrences and causes of waterborne-disease outbreaks (WBDOs). This surveillance system is the primary source of data concerning the scope and effects of waterborne disease outbreaks on persons in the United States. REPORTING PERIOD COVERED: This summary includes data on WBDOs associated with drinking water that occurred during January 2001-December 2002 and on three previously unreported outbreaks that occurred during 2000. DESCRIPTION OF SYSTEM: Public health departments in the states, territories, localities, and the Freely Associated States are primarily responsible for detecting and investigating WBDOs and voluntarily reporting them to CDC on a standard form. The surveillance system includes data for outbreaks associated with both drinking water and recreational water; only outbreaks associated with drinking water are reported in this summary. RESULTS: During 2001-2002, a total of 31 WBDOs associated with drinking water were reported by 19 states. These 31 outbreaks caused illness among an estimated 1,020 persons and were linked to seven deaths. The microbe or chemical that caused the outbreak was identified for 24 (77.4%) of the 31 outbreaks. Of the 24 identified outbreaks, 19 (79.2%) were associated with pathogens, and five (20.8%) were associated with acute chemical poisonings. Five outbreaks were caused by norovirus, five by parasites, and three by non-Legionella bacteria. All seven outbreaks involving acute gastrointestinal illness of unknown etiology were suspected of having an infectious cause. For the first time, this MMWR Surveillance Summary includes drinking water-associated outbreaks of Legionnaires disease (LD); six outbreaks of LD occurred during 2001-2002. Of the 25 non-Legionella associated outbreaks, 23 (92.0%) were reported in systems that used groundwater sources; nine (39.1%) of these 23 groundwater outbreaks were associated with private noncommunity wells that were not regulated by EPA. INTERPRETATION: The number of drinking water-associated outbreaks decreased from 39 during 1999-2000 to 31 during 2001-2002. Two (8.0%) outbreaks associated with surface water occurred during 2001-2002; neither was associated with consumption of untreated water. The number of outbreaks associated with groundwater sources decreased from 28 during 1999-2000 to 23 during 2001-2002; however, the proportion of such outbreaks increased from 73.7% to 92.0%. The number of outbreaks associated with untreated groundwater decreased from 17 (44.7%) during 1999-2000 to 10 (40.0%) during 2001-2002. Outbreaks associated with private, unregulated wells remained relatively stable, although more outbreaks involving private, treated wells were reported during 2001-2002. Because the only groundwater systems that are required to disinfect their water supplies are public systems under the influence of surface water, these findings support EPA's development of a groundwater rule that specifies when corrective action (including disinfection) is required. PUBLIC HEALTH ACTION: CDC and EPA use surveillance data 1) to identify the types of water systems, their deficiencies, and the etiologic agents associated with outbreaks and 2) to evaluate the adequacy of technologies for providing safe drinking water. Surveillance data are used also to establish research priorities, which can lead to improved water-quality regulations. CDC and EPA recently completed epidemiologic studies that assess the level of waterborne illness attributable to municipal drinking water in nonoutbreak conditions. The decrease in outbreaks in surface water systems is attributable primarily to implementation of provisions of EPA rules enacted since the late 1980s. Rules under development by EPA are expected to protect the public further from microbial contaminants while addressing risk tradeoffs of disinfection byproducts in drinking water.

Blacklow, N. R. and G. Cukor (1981). "Viral gastroenteritis." N Engl J Med 304(7): 397-406.
	
Blacklow, N. R. and G. Cukor (1982). "Norwalk virus: a major cause of epidemic gastroenteritis." Am J Public Health 72(12): 1321-03.
	
Blacklow, N. R., G. Cukor, et al. (1979). "Immune response and prevalence of antibody to Norwalk enteritis virus as determined by radioimmunoassay." J. Clin. Microbiol. 10(6): 903-909.
	A solid-phase microtiter radioimmunoassay was established for the detection of Norwalk virus and its antibody, with clinical materials from human volunteers previously studied in Massachusetts as reagents. A study of 308 Massachusetts residents showed that serum antibody to Norwalk agent was rarely present during childhood but was detectable in approximately 50% of adults. All volunteers inoculated with Norwalk virus who developed illness seroconverted (10/10), whereas only one-third (5/15) of nonill volunteers seroconverted (P = 0.0009). The 10 nonill, nonseroconverting subjects had undetectable to low preexisting antibody levels. Paradoxically, 10/13 subjects with preexisting antibody became ill, whereas 17/25 lacking antibody did not (P = 0.009). All 3 subjects with preexisting anti-Norwalk radioimmunoassay blocking activity in duodenal intraluminal fluids became ill, whereas only 5/11 lacking such activity developed illness (P = 0.15). These data further support the unique concept that some individuals are susceptible to repeated infections with this agent, whereas others are incapable of developing infection.

Blacklow, N. R. and H. B. Greenberg (1991). "Viral gastroenteritis." New England Journal of Medicine 324(25): 252-264.
	
Blacklow, N. R., J. E. Herrmann, et al. (1987). "Immunobiology of Norwalk virus." Ciba Found Symp 128: 144-61.
	Clinical immunity to Norwalk virus in inoculated human volunteers appears to be unusual for gastroenteritis viruses, as certain individuals are repeatedly ill on long-term virus rechallenge and others remain persistently well. In these volunteers there is a paradoxical inverse correlation between the prechallenge serum (and jejunal fluid) Norwalk antibody level (measured by radioimmunoassay) and resistance to illness, suggesting that non-immunological factors, perhaps genetic, may be important in determining resistance. Most reported naturally occurring Norwalk disease outbreaks in developed nations also show that humoral antibody fails to correlate with immunity to infection. The unusual pattern of clinical immunity to Norwalk virus indicates a need for caution in the development of vaccines against this agent as well as a need for additional information on its immunobiological characteristics. The virus is known to contain a single protein, like the caliciviruses. Recently we have found evidence for at least a one-way serological cross-relatedness between Norwalk virus and human calicivirus. Twelve of 20 paired sera from ill patients in outbreaks due to calicivirus strain UK4 seroconverted to Norwalk virus by radioimmunoassay and two of eight paired sera from UK2 outbreaks showed seroconversion. Future studies of outbreaks caused by various calicivirus strains should be designed to correlate acute-phase serum antibody titres to Norwalk virus with clinical susceptibility and immunity to infection.

Blackman, E., S. Binder, et al. (1997). "Cryptosporidiosis in HIV-infected patients: diagnostic sensitivity of stool examination, based on number of specimens submitted." American Journal of Gastroenterology 92(3): 451-453.
	OBJECTIVES: To determine the optimal number of stool specimens needed for the diagnosis of cryptosporidiosis. METHODS: Four hundred thirty-five admissions were reviewed (291 patients) in which stool specimens were examined for Cryptosporidium parvum oocysts (mean of 1.47 specimens per admission), using a modified acid-fast stain. The diagnostic yield of each specimen was determined. RESULTS: Cryptosporidium parvum oocysts were found in 81 of 435 admissions (18.6%). Ninety-six percent of the positive cases were detected on the first stool specimen analysis, and 100% were detected by the second specimen. CONCLUSIONS: Examination of one specimen is generally appropriate for the diagnosis of cryptosporidiosis in a hospitalized patient with AIDS presenting with diarrhea. Examination of a second specimen may be appropriate if the first specimen is negative and there is a high clinical index of suspicion. 

Blackmer, F., K. A. Reynolds, et al. (2000). "Use of Integrated  Cell Culture-PCR To Evaluate the Effectiveness of Poliovirus Inactivation by  Chlorine." Applied  and Environmental Microbiology 66(5): 2267-2268.
	
Blackwell, J. H. (1976). "Survival of foot-and-mouth disease virus in cheese." Journal of Dairy Science 59(9): 1574-1579.
	Persistence of foot-and-mouth disease virus during the manufacture of Cheddar, Mozzarella, Camembert cheese prepared from milk of cows experimentally infected with the virus was studied. Cheese samples were made on a laboratory scale with commercial lactic acid starter cultures and the microbial protease MARZYME as a coagulant. Milk was heated at different temperatures for different intervals before it was made into cheese. Food-and-mouth disease virus survived the acidic conditions of Cheddar and Camembert cheese processing but not that of Mozzarella. Foot-and-mouth disease virus survived processing but not curing for 30 days in Cheddar cheese preparaed from heated milk. However, the virus survived curing for 60 days but not for 120 days in cheese (pH 5) prepared from unheated milk. Foot-and-mouth disease virus survived in Camembert cheese (pH 5) for 21 days at 2 C but not for 35 days. 

Blackwell, J. H. (1980). "Internationalism and survival of foot-and-mouth disease virus in cattle and food products." Journal of Dairy Science 63(6): 1019-1030.
	Foot-and-mouth disease is a serious world-wide economic disease of livestock and diverse animal species. The closing of borders to infected countries is a frequent aftermath of disease outbreaks. Historically, animals and animal products have been implicated as vehicles for transmission of the disease. Control programs encompass stringent importation policies, vaccination, quarantine, and slaughter. Joint efforts have been instituted successfully in previous control campaigns and would be the logical approach to large-scale eradication schemas. 

Blackwell, J. H. (1984). "Foreign animal disease agent survival in animal products: recent developments." J Am Vet Med Assoc 184(6): 674-9.
	
Blackwell, J. H. and J. L. Hyde (1976). "Effect of heat on foot-and-mouth disease virus (FMDV) in the components of milk from FMDV-infected cows." Journal of Hygiene, Cambridge 77: 77-83.
	not available

Blackwell, J. H., E. J. Nolan, et al. (1988). "Total caloric input of a thermal process as an index of lethality for foot-and-mouth disease virus." Journal of Food Science 53(1): 185-190.
	Because significant quantities of foot-and-mouth disease virus undetectable by cell culture infectivity assay can persist in infected tissues throughout thermal processing, classical methods for measuring virus inactivation are difficult to achieve. This study was undertaken to observe the lethality of a given process rather than determining a constant for process time for a given lethality. Thermal diffusivities (alpha) and one-dimensional heat flux (Q) were determined for three thermal processes used in processing of beef and pork products. Foot-and-mouth disease virus survived in ground beef cooked in flexible nylon thermal processing tubes to core temperatures of 63 degrees C (892 kcal/m2) in 1.2 hr and 71.2 degrees C (1004 kcal/m2) in 1.45 hr; however, the virus did not survive after processing to a core temperature of 79.4 degrees C (1363 kcal/m2) in 2.0 hr.

Blackwell, J. H., D. Rickansrud, et al. (1982). "Effect of thermal processing on the survival of foot-and-mouth disease virus in ground meat." Journal of Food Science 47: 388-92.
	Foot-and-mouth disease virus was examined for its stability during cooking in tissues from infected cattle. The O1 (CANEFA 2) serotype of foot-and-mouth disease virus survived in lymph node tissues after heating for 2 hr at 69ºC, for 1 hr but not for 2 hr at 82ºC, and for 15 min but not for 0.5 hr at 90ºC. Incorporation of 1% NaCl into suspensions of infected lymph nodes enhanced viral survival after heating for 0.5 hr but not for 1 hr at 90ºC. The virus did not survive in either ground beef or meatballs contaminated with infected lymph node tissue, when processed to internal temperatures of 93.3, 96.1 or 98.8ºC using commercial thermal processing procedures. Accurate temperature measurements were achieved with a temperature sensitive indicator disc developed in this study.

Blackwell, J. H., S. Wool, et al. (1981). "Vesicular exocytosis of foot-and-mouth disease virus from mammary gland secretory epithelium of infected cows." Journal of General Virology 56(1): 207-212.
	Foot-and-mouth disease virus particles were observed by electron microscopy in the cytoplasma of alveolar secretory cells of the bovine mammary gland after contact exposure of uninfected cows to pits with foot-and-mouth disease. Virus, contained in membrane-limited vesicles, was released from the basal and peranuclear portions of the cells into the intracellular and extracellular spaces by an exocytotic mechanism similar to that of the release of th milk-fat globule. Virus was released into the lumen from the apical portion of the cell both by membrane-limited vesicles and by the merocrinal exocytosis of casein-associated virus. The lytic release of virus was observed in 20% of the preparations observed

Blanch, E. W., L. Hecht, et al. (2002). "Molecular structures of viruses from Raman optical activity." J Gen Virol 83(Pt 10): 2593-600.
	A vibrational Raman optical activity (ROA) study of a range of different structural types of virus exemplified by filamentous bacteriophage fd, tobacco mosaic virus, satellite tobacco mosaic virus, bacteriophage MS2 and cowpea mosaic virus has revealed that, on account of its sensitivity to chirality, ROA is an incisive probe of their aqueous solution structures at the molecular level. Protein ROA bands are especially prominent from which, as we have shown by comparison with the ROA spectra of proteins with known structures and by using a pattern recognition program, the folds of the major coat protein subunits may be deduced. Information about amino acid side-chain conformations, exemplified here by the determination of the sign and magnitude of the torsion angle chi(2,1) for tryptophan in fd, may also sometimes be obtained. By subtracting the ROA spectrum of the empty protein capsid (top component) of cowpea mosaic virus from those of the intact middle and bottom-upper components separated by means of a caesium chloride density gradient, the ROA spectrum of the viral RNA was obtained, which revealed that the RNA takes up an A-type single-stranded helical conformation and that the RNA conformations in the middle and bottom-upper components are very similar. This information is not available from the X-ray crystal structure of cowpea mosaic virus since no nucleic acid is visible.

Blanton, L. H., S. M. Adams, et al. (2006). "Molecular and epidemiologic trends of caliciviruses associated with outbreaks of acute gastroenteritis in the United States, 2000-2004." J Infect Dis 193(3): 413-21.
	Between July 2000 and June 2004, fecal specimens from 270 outbreaks of acute gastroenteritis were sent to the Centers for Disease Control and Prevention by local or state health departments for calicivirus testing. Of the 226 outbreaks that met the criteria for inclusion in the present study, caliciviruses were detected in 184 (81%) by reverse-transcription polymerase chain reaction and nucleotide sequencing. Nursing homes, retirement centers, and hospitals were the most frequently reported settings, and person-to-person contact was the most common mode of transmission, followed by foodborne spread. Overall, genogroup II norovirus (NoV) strains were the most abundant (79%), followed by genogroup I NoV strains (19%) and sapovirus (2%). Nucleotide-sequence analysis indicated a great diversity of NoV strains and implicated the emergence of one particular sequence variant in outbreaks occurring between July 2002 and June 2003. The public health impact of caliciviruses will not be fully appreciated, nor will interventions be completely evaluated, until methods to detect these viruses are more routinely used.

Bloch, A. B., S. L. Stramer, et al. (1990). "Recovery of hepatitis A virus from a water supply responsible for a common source outbreak of hepatitis A." American Journal of Public Health 80(4): 428-430.
	An outbreak of hepatitis A occurred in a north Georgia trailer park served by a private well. Of 18 residents who were serosusceptible to hepatitis A virus (HAV), 16 (89%) developed hepatitis A. Well water samples were collected 3 months after illness onset in the index case and 28 days after illness onset in the last trailer park resident. Hepatitis A virus antigen (HAVAg) was detected in the samples by enzyme immunoassay from three of the five cell lines following two 30-day passages and from a fourth cell line following a third passage of 21 days. 

Blomqvist, S., A. L. Bruu, et al. (2003). "Characterization of a recombinant type 3/type 2 poliovirus isolated from a healthy vaccinee and containing a chimeric capsid protein VP1." J Gen Virol 84(Pt 3): 573-80.
	A Sabin 3/Sabin 2/Sabin 3 (S3/2/3) intertypic recombinant poliovirus was isolated from a faecal specimen from a 2-year-old healthy boy approximately 12 weeks after administration of oral poliovirus vaccine. The first recombination junction was in the genomic region encoding the VP1 capsid protein between nucleotide positions 3274 and 3285 (numbering according to Sabin 3) and the second was in the RNA polymerase region (nucleotide positions 6824 and 6825). The recombination had introduced six Sabin 2-derived amino acids into the Sabin 3 capsid environment in the carboxyl terminus of VP1. The complete genome of the recombinant virus differed from corresponding parental Sabin strains at 33 nucleotide positions, nine of them resulting in an amino acid substitution. Four substitutions were in the capsid proteins and five were in the region encoding the non-structural proteins. One amino acid was changed in the antigenic site 2B and two in site 3B. In addition, the whole antigenic site 3A was replaced by Sabin 2-specific amino acids, but the antigenic characteristics of the S3/2/3 did not show type 2-specific features. Neutralizing antibody titres in sera from Finnish children immunized with the inactivated poliovirus vaccine were not lower against the recombinant virus than against Sabin 3. Our results suggest that the chimeric virus was most likely generated by recombination events in the vaccinee, rather than representing progeny of circulating vaccine-derived virus.

Blomqvist, S., C. Savolainen, et al. (2004). "Characterization of a highly evolved vaccine-derived poliovirus type 3 isolated from sewage in Estonia." J Virol 78(9): 4876-83.
	Two types of vaccine-derived polioviruses have been recently designated to emphasize the different origins of the evolved viruses: circulating vaccine-derived polioviruses (cVDPV) associated with outbreaks of paralytic disease and strains isolated from chronically infected immunodeficient individuals (iVDPV). We describe here a type 3 VDPV (PV3/EST/02/E252; later E252) isolated from sewage collected in Tallinn, Estonia, in October 2002. Due to aberrant properties in subtyping, the virus was subjected to detailed characterization. Partial genomic sequencing suggested that the closest relative was the oral vaccine strain PV3/Sabin, but the two virus strains shared only 86.7% of the 900 nucleotides (nt) coding for the capsid protein VP1. Phylogenetic analysis of the nearly complete genome [nt 19 to poly(A)] revealed multiple nucleotide substitutions throughout the genome and a possible Sabin 3/Sabin 1-recombination junction site in the 2C coding region. A calculation based on the estimated mutation frequency of the P1 region of polioviruses suggested that the E252 virus might have replicated in one or more individuals for approximately 10 years. No persons chronically excreting poliovirus are known in Estonia. Amino acid substitutions were seen in all known antigenic sites, which was consistent with the observed aberrant antigenic properties of the virus demonstrated by both monoclonal antibodies and human sera from vaccinated children. In spite of the apparent transmission potential, no evidence was obtained for circulation of the virus in the Estonian population.

Boardman, G. D., T. R. McBrayer, et al. (1989). "Detection and occurrence of waterborne bacterial and viral pathogens." J. Water Poll. Control Fed. 61(6): 1097-1109.
	
Boccia, D., A. E. Tozzi, et al. (2002). "Waterborne outbreak of Norwalk-like virus gastroenteritis at a tourist resort, Italy." Emerg Infect Dis 8(6): 563-8.
	In July 2000, an outbreak of gastroenteritis occurred at a tourist resort in the Gulf of Taranto in southern Italy. Illness in 344 people, 69 of whom were staff members, met the case definition. Norwalk-like virus (NLV) was found in 22 of 28 stool specimens tested. The source of illness was likely contaminated drinking water, as environmental inspection identified a breakdown in the resort water system and tap water samples were contaminated with fecal bacteria. Attack rates were increased (51.4%) in staff members involved in water sports. Relative risks were significant only for exposure to beach showers and consuming drinks with ice. Although Italy has no surveillance system for nonbacterial gastroenteritis, no outbreak caused by NLV has been described previously in the country.

Bockstahler, L. E. and C. D. Lytle (1971). "X-ray-enhanced reactivation of ultraviolet-irradiated human virus." J Virol 8(4): 601-2.
	
Bodian, D. (1956). "Simplified method of dispersion of monkey kidney cells with trypsin." Virology 2(4): 575-6.
	
Bodian, D. (1957). Mechanisms of infection with polioviruses. Cellular Biology, Nucleic Acids, and Viruses. O. V. S. W. (Ed.). New York, New York Academy of Sciences: 59-72.
	
Boeye, A. and B. Rombaut (1992). "The proteins of poliovirus." Prog Med Virol 39: 139-66.
	
Bofill-Mas, S., N. Albinana-Gimenez, et al. (2006). "Quantification and stability of human adenoviruses and polyomavirus JCPyV in wastewater matrices." Appl Environ Microbiol 72(12): 7894-6.
	Human adenoviruses (HAdV) and human polyomavirus JCPyV have been previously proposed as indicators of fecal viral contamination in the environment. Different wastewater matrices have been analyzed by applying real-time quantitative PCR procedures for the presence, quantity, and stability of a wide diversity of excreted HAdV and JCPyV. High quantities of HAdV and JCPyV were detected in sewage, effluent wastewater, sludge, and biosolid samples. Both viruses showed high stability in urban sewage. These results confirm the suitability of both viruses as indicators of human fecal viral pollution.

Bofill-Mas, S., P. Clemente-Casares, et al. (2003). "Analysis of the excreted JC virus strains and their potential oral transmission." J Neurovirol 9(4): 498-507.
	JC virus (JCV) particles have been detected in urban sewage of divergent geographical areas. In this study, the authors evaluate the genetic characteristics and the infective capabilities of JCV strains in relation to the potential oral transmission of JCV in the population. JCV strains excreted in urine and detected in sewage have been described as presenting archetypal structure of the regulatory region of the viral genome. The regulatory region of JCV viral particles detected in two urban sewage samples have been cloned and characterized. From a total of 40 clones tested, 39 presented archetypal-like regulatory regions, whereas 1 of the clones analyzed presented a tandem repeated structure. Archetypal strains present in the urine of a pregnant woman were able to infect SVG cells, producing infectious virions, as demonstrated by confirmative cell culture, electron microscopy, and in situ DNA hybridization. This is the first description of archetypal JCV productive infection of SVG cells. SVG cells were also successfully infected with Mad-4 JCV viral particles subjected to pH 3 for 1 h at 37 degrees C and to 10 microg/ml of trypsin in the same conditions. A decrease in the viral progeny production was observed when Mad-4 was subjected to acidic pH. Mad-4 did not produce any detectable infection in the enteric cell line CaCo-2. The oral route could represent a significant route of transmission of JCV infections because JCV virions have demonstrated relative resistance in the environment and to some of the conditions present in the gastrointestinal tract. The archetypal strains commonly detected in the environment may be implicated in the transmission of JCV among the population. Sporadic infection with strains presenting tandem repeated structures may have implications in pathogenicity.

Bofill-Mas, S., M. Formiga-Cruz, et al. (2001). "Potential transmission of human polyomaviruses through the gastrointestinal tract after exposure to virions or viral DNA." J Virol 75(21): 10290-9.
	The mechanism of human-to-human transmission of the polyomaviruses JC virus (JCV) and BK virus (BKV) has not been firmly established with regard to possible human exposure. JCV and BKV have been found in sewage samples from different geographical areas in Europe, Africa, and the United States, with average concentrations of 10(2) to 10(3) JCV particles/ml and 10(1) to 10(2) BKV particles/ml. Selected polyomavirus-positive sewage samples were further characterized. The JCV and BKV present in these samples were identified by sequencing of the intergenic region (the region found between the T antigen and VP coding regions) of JCV and the VP1 region of BKV. The regulatory region of the JCV and BKV strains found in sewage samples presented archetypal or archetype-like genetic structures, as described for urine samples. The stability (the time required for a 90% reduction in the virus concentration) of the viral particles in sewage at 20 degrees C was estimated to be 26.7 days for JCV and 53.6 days for BKV. The presence of JCV in 50% of the shellfish samples analyzed confirmed the stability of these viral particles in the environment. BKV and JCV particles were also found to be stable at pH 5; however, treatment at a pH lower than 3 resulted in the detection of free viral DNA. Since most humans are infected with JCV and BKV, these data indicate that the ingestion of contaminated water or food could represent a possible portal of entrance of these viruses or polyomavirus DNA into the human population.

Bofill-Mas, S. and R. Girones (2001). "Excretion and transmission of JCV in human populations." J Neurovirol 7(4): 345-9.
	The potential transmission of JCV through the environment has been analyzed by studying the JC viruses present in raw sewage of urban populations from widely divergent geographical areas. High numbers of JCV were found. JCV was detected in 98% (51/52) of sewage samples from different geographical areas in Europe, Africa, and USA by applying a Nested-PCR procedure. The mean estimated concentration of JCV in sewage was of 10(2)-10(3) viral particles/ml. Sequence analysis shows that JCV found in environmental samples present an archetypal structure in the regulatory region as it has been described in urine samples. Cerebrospinal fluid samples (CSF) of PML (progressive multifocal leucoencephalopathy) patients were also analyzed as control samples in this study presenting tandem repeats and rearrangements at the regulatory region (RR). Sequence analysis of the intergenic region (IGR) allowed the typification and phylogenetic analysis of the JCV sequences detected in sewage. JC viral particles were also found to be stable in sewage samples at 20 degrees C for more than 70 days. This data suggest the idea that the intake of water or food contaminated with JCV could constitute a portal of entry for the virus or the viral DNA to the human organism.

Bofill-Mas, S. and R. Girones (2003). "Role of the environment in the transmission of JC virus." J Neurovirol 9 Suppl 1: 54-8.
	JC virus is etiologically associated with a fatal demyelinating disease known as PML. JCV produces persistent infections in the kidney and is excreted in the urine of healthy individuals and in the urine of PML patients. The characteristics of the JCV excreted in the environment have been studied by analyzing sewage samples from divergent geographical areas. The intergenic region of JCV strains detected in the sewage of Barcelona (Spain), Umea (Sweden), Nancy (France), Pretoria (South Africa), Patras (Greece), Cairo (Egypt), Washington, D.C. (USA), and diverse areas of Northern India has been sequenced, and the phylogenetic analysis showed their relationships with JCV strains previously described in urine or clinical samples in these geographic areas. The JCV regulatory region of the JCV DNA detected in sewage presented archetypal or archetypal-like regulatory regions with the exception of one of the twenty clones obtained from a sewage sample of the area of Washington, D.C. that presented a tandem repeated structure. Infectivity studies showed that archetypal JCV present in the urine of a pregnant woman productively infected SVG cells. Also JC viral particles showed considerable stability in sewage at 20 degrees C and in front of treatments with acidic pH and trypsin. The high prevalence of JCV in urine and in sewage and the stability of the viral particles observed suggests that contaminated water, food, and fomites could be the vehicles of JCV transmission through the oral route. Virions partially degraded or noninfectious could be a source of JCV DNA and may represent an additional mechanism of entry of viral genes into cells.

Bofill-Mas, S., S. Pina, et al. (2000). "Documenting the epidemiologic patterns of polyomaviruses in human populations by studying their presence in urban sewage." Appl Environ Microbiol 66(1): 238-45.
	This is the first description, to our knowledge, of the distribution of human polyomavirus and simian virus 40 (SV40) in urban sewage. Using a nested-PCR procedure, we report the detection of human polyomaviruses JC virus (JCV) and BK virus (BKV) but not SV40 in a high percentage of urban sewage samples obtained from widely divergent geographical areas in Europe and Africa. For a total of 28 samples analyzed, JCV was detected in 26, BKV was detected in 22, and none was positive for SV40. All geographical areas showed a high prevalence of these viruses with mean estimated values of JC viral particles per ml on the order of 10(3) in Barcelona (Spain) and Nancy (France) and 10(2) in Pretoria (South Africa) and Umea (Sweden) and mean values of BK viral particles on the order of 10(2) in Pretoria and Barcelona and 10(1) in Nancy and Umea. This compares with estimated mean values of 10(2) to 10(3) for human adenovirus that was evaluated as a control. Nucleotide sequence analysis of the amplified DNA from some of the samples is also presented and represents the sequence of the most abundant JC and BK viral strains in these samples. The nucleotide sequence of the JCV detected was also analyzed in a phylogenetic study and for genomic characterization in the regulatory region. This study has shown that human polyomaviruses are spread in high concentrations in the sewage of different geographical areas and are present in contaminated environments. The frequency and concentration of JCV detected in the environment and the absence of described animal hosts suggest that JCV may be useful as a marker for fecal pollution of anthropogenic origin. The results also support the idea previously described that the strains of JCV are closely related to the ethnic origin of the population studied. The procedure applied should also be useful in future studies of population patterns of viral excretion and as a tool in epidemiological studies for the detection of changes in the prevalence of specific viral pathogens.

Boher, S., C. Beril, et al. (1991). "Comparison of Two Methods for the Recovery of Rotavirus from Mussels and Oysters." Water Science and Technology 24(2): 423-426.
	
Bohm, H. O. and H. Krebs (1974). "[Isolation of foot-and-mouth-disease virus from organs of infected, slaughtered sheep]." Berl Munch Tierarztl Wochenschr 87(21): 410-2.
	
Bollback, J. P. and J. P. Huelsenbeck (2001). "Phylogeny, genome evolution, and host specificity of single-stranded RNA bacteriophage (family Leviviridae)." J Mol Evol 52(2): 117-28.
	Bacteriophage of the family Leviviridae have played an important role in molecular biology where representative species, such as Q beta and MS2, have been studied as model systems for replication, translation, and the role of secondary structure in gene regulation. Using nucleotide sequences from the coat and replicase genes we present the first statistical estimate of phylogeny for the family Leviviridae using maximum-likelihood and Bayesian estimation. Our analyses reveal that the coliphage species are a monophyletic group consisting of two clades representing the genera Levivirus and Allolevivirus. The Pseudomonas species PP7 diverged from its common ancestor with the coliphage prior to the ancient split between these genera and their subsequent diversification. Differences in genome size, gene composition, and gene expression are shown with a high probability to have changed along the lineage leading to the Allolevivirus through gene expansion. The change in genome size of the Allolevivirus ancestor may have catalyzed subsequent changes that led to their current genome organization and gene expression.

Bolten, R., D. Egger, et al. (1998). "Intracellular localization of poliovirus plus- and minus-strand RNA visualized by strand-specific fluorescent In situ hybridization." J Virol 72(11): 8578-85.
	The time courses of poliovirus plus- and minus-strand RNA synthesis in infected HEp-2 cells were monitored separately, using a quantitative RNase assay. In parallel, viral RNA and proteins were located in situ by confocal microscopy within cells fixed by a protocol determined to retain their native size and shape. Plus- and minus-strand RNAs were visualized by fluorescent in situ hybridization (FISH) with strand-specific riboprobes. The probes were labelled with different fluorochromes to allow for the simultaneous detection of plus- and minus-strand RNA. The FISH experiments showed minus-strand RNA to be present in distinct, regularly sized, round structures throughout the viral replication cycle. Plus-strand RNA was found in the same structures and also in smaller clusters of vesicles. Association of viral RNA with membranes was demonstrated by combining FISH with immunofluorescence (IF) detection of the viral 2B- and 2C-containing P2 proteins, which are known to be markers for virus-induced membranes. At early times postinfection, the virus-induced membranous structures were distributed through most of the cytoplasm, whereas around peak RNA synthesis, both RNA-associated membranous structures migrated to the center of the cell. During this process, the plus- and minus-strand-containing larger structures stayed as recognizable entities, whereas the plus-strand-containing granules coalesced into a juxtanuclear area of membranous vesicles. An involvement of Golgi-derived membranes in the formation of virus-induced vesicles and RNA synthesis early in infection was investigated by IF with 2C- and Golgi-specific antibodies.

Bon, F., K. Ambert-Balay, et al. (2005). "Molecular epidemiology of caliciviruses detected in sporadic and outbreak cases of gastroenteritis in France from December 1998 to February 2004." J Clin Microbiol 43(9): 4659-64.
	We compiled sequence and epidemiological data from 172 caliciviruses detected in France from December 1998 to February 2004 in sporadic and outbreak cases. The results showed a cocirculation of strains with a majority of genogroup II (GII) noroviruses. Three groups of noroviruses, not detected before in our laboratory, emerged and spread during the period: the recombinant GGIIb and Norwalk-related strains not amplified in the polymerase gene in 2000 and a new Lordsdale variant in 2002. We observed that (i) GII-4 noroviruses were predominant in nursing home and hospital outbreaks but rare in oyster- and water-related outbreaks despite continuous circulation in the population; (ii) at the opposite, genogroup I strains were detected in the majority of environmental outbreaks; (iii) several strains were frequently found in oyster- and water-linked outbreaks (up to seven), whereas one single strain was detected when transmission was from person to person; and (iv) whereas GII noroviruses were predominant in sporadic cases where patients were under 15 years of age, GI strains were more frequent in outbreaks occurring in this age group. Finally, from a methodology point of view, this compilation shows that detection and characterization in the polymerase gene are not adequate in a significant number of cases and should be completed by amplification and sequencing in the capsid gene.

Bon, F., P. Fascia, et al. (1999). "Prevalence of group A rotavirus, human calicivirus, astrovirus, and adenovirus type 40 and 41 infections among children with acute gastroenteritis in Dijon, France." J Clin Microbiol 37(9): 3055-8.
	Group A rotaviruses, human caliciviruses, astroviruses, and adenovirus types 40 and 41 were detected by enzyme immunoassay or reverse transcription-PCR in 61, 14, 6, and 3% of stool specimens from 414 children consulting for gastroenteritis between 1995 and 1998. These data highlight the importance of caliciviruses in infantile gastroenteritis. Among these, Norwalk-like viruses belonging to genogroup II were predominant.

Boom, R., C. J. A. Sol, et al. (1990). "Rapid and simple method for purification of nucleic acids." Journal of Clinical Microbiology 28(3): 495-503.
	We have developed a simple, rapid, and reliable protocol for the small-scale purification of DNA and RNA from, e.g., human serum and urine. The method is based on the lysing and nuclease-inactivating properties of the chaotropic agent guanidinium thiocyanate together with the nucleic acid-binding properties of silica particles or diatoms in the presence of this agent. By using size-fractionated silica particles, nucleic acids (covalently closed circular, relaxed circular, and linear double-stranded DNA; single-stranded DNA; and rRNA) could be purified from 12 different specimens in less than 1 h and were recovered in the initial reaction vessel. Purified DNA (although significantly sheared) was a good substrate for restriction endonucleases and DNA ligase and was recovered with high yields (usually over 50%) from the picogram to the microgram level. Copurified rRNA was recovered almost undegraded. Substituting size-fractionated silica particles for diatoms (the fossilized cell walls of unicellular algae) allowed for the purification of microgram amounts of genomic DNA, plasmid DNA, and rRNA from cell-rich sources, as exemplified for pathogenic gram-negative bacteria. In this paper, we show representative experiments illustrating some characteristics of the procedure which may have wide application in clinical microbiology. 

Boone, S. A. and C. P. Gerba (2007). "Significance of fomites in the spread of respiratory and enteric viral disease." Appl Environ Microbiol 73(6): 1687-96.
	
Borchardt, M. A., P. D. Bertz, et al. (2003). "Incidence of enteric viruses in groundwater from household wells in Wisconsin." Appl Environ Microbiol 69(2): 1172-80.
	Recent studies on the contamination of groundwater with human enteric viruses have focused on public water systems, whereas little is known about the occurrence of viruses in private household wells. The objective of the present study was to estimate the incidence of viruses in Wisconsin household wells located near septage land application sites or in rural subdivisions served by septic systems. Fifty wells in seven hydrogeologic districts were sampled four times over a year, once each season. Reverse transcriptase PCR (RT-PCR), followed by Southern hybridization, was used to detect enteroviruses, rotavirus, hepatitis A virus (HAV), and Norwalk-like viruses (NLVs). In addition, cell culture was used to detect culturable enteroviruses. Companion water samples were collected for total coliforms, Escherichia coli, fecal enterococci, F-specific RNA coliphages, nitrate, and chloride analyses. Among the 50 wells, four (8%) were positive for viruses by RT-PCR. Three wells were positive for HAV, and the fourth well was positive for both rotavirus and NLV in one sample and an enterovirus in another sample. Contamination was transient, since none of the wells was virus positive for two sequential samples. Culturable enteroviruses were not detected in any of the wells. Water quality indicators were not statistically associated with virus occurrence, although some concordance was noted for chloride. The present study is the first in the United States to systematically monitor private household wells for virus contamination and, combined with data for public wells, provides further insight on the extent of groundwater contamination with human enteric viruses.

Borchardt, M. A., N. L. Haas, et al. (2004). "Vulnerability of drinking-water wells in La Crosse, Wisconsin, to enteric-virus contamination from surface water contributions." Appl Environ Microbiol 70(10): 5937-46.
	Human enteric viruses can contaminate municipal drinking-water wells, but few studies have examined the routes by which viruses enter these wells. In the present study, the objective was to monitor the municipal wells of La Crosse, Wisconsin, for enteric viruses and determine whether the amount of Mississippi River water infiltrating the wells was related to the frequency of virus detection. From March 2001 to February 2002, one river water site and four wells predicted by hydrogeological modeling to have variable degrees of surface water contributions were sampled monthly for enteric viruses, microbial indicators of sanitary quality, and oxygen and hydrogen isotopes. (18)O/(16)O and (2)H/(1)H ratios were used to determine the level of surface water contributions. All samples were collected prior to chlorination at the wellhead. By reverse transcription-PCR (RT-PCR), 24 of 48 municipal well water samples (50%) were positive for enteric viruses, including enteroviruses, rotavirus, hepatitis A virus (HAV), and noroviruses. Of 12 river water samples, 10 (83%) were virus positive by RT-PCR. Viable enteroviruses were not detected by cell culture in the well samples, although three well samples were positive for culturable HAV. Enteroviruses detected in the wells by RT-PCR were identified as several serotypes of echoviruses and group A and group B coxsackieviruses. None of the well water samples was positive for indicators of sanitary quality, namely male-specific and somatic coliphages, total coliform bacteria, Escherichia coli, and fecal enterococci. Contrary to expectations, viruses were found in all wells regardless of the level of surface water contributions. This result suggests that there were other unidentified sources, in addition to surface water, responsible for the contamination.

Borneff, J., R. Hassinger, et al. (1988). "[The distribution of microorganisms in household kitchens. I. Problems, experiments, results]." Zentralbl Bakteriol Mikrobiol Hyg [B] 186(1): 1-29.
	Epidemiological investigations have demonstrated that insufficient hygiene in households results in increasing health hazards. In order to be able to recommend ways to disrupt infection chains it was necessary to explore the most important pathways of cross-contamination. Housewives without special training were instructed to prepare a complete meal, in the kitchen of a modern, vacant apartment. Among the raw products provided was minced meat, contaminated with Sarcinae (unbeknown to the housewives) in a quantitative manner. When cooking and cleaning procedures were completed we analysed household utensils and surfaces by Rodac impressions and swabs. The test organisms could be detected on all inspected surfaces and on the dining-table with albeit different frequencies. The following locations showed an especially high degree of cross-contamination: a) working-surfaces, especially boards of wood and plastics. b) cutting-machines, c) kitchen-machines. These results agree with literature data. By careful disinfection, i.e. by application of a 0.5% solution of hypochlorite, the contaminations could be removed. We assessed this when arranging the kitchen for the next test. Since it is impossible to practise disinfection procedures in a household kitchen on the same scale as in an operating room, we tried to achieve at least a limited disinfection by household cleansers with germicidal properties. In our opinion a minimum reduction of five log stages, demanded in the medical area, can not be achieved in a household kitchen and indeed it is not necessary. A reduction of the microbial counts to 10% of the original value would already be useful, as toxic levels of microbial counts will be reached later especially when there is simultaneous refrigeration. Correct dosage proved to be one of the main practical problems because a discrepancy exists between the low concentration of tensids, necessary for cleaning, and the relatively high dose necessary for germ-killing compounds. Diluted DOMESTOS proved to be a cleaning agent and germicide, but was, however, blamed for chlorine odour, especially when diluted with warm water. A greater acceptance level was reached with a peroxide-containing cleanser, which, however, was not sufficiently germicidal, when applied in diluted form. The concentrated formulation was more effective in everyday experience, but for this housewives had to wear rubber gloves. This was reported to be complicated and uncomfortable, and indeed the search for better formulations must be continued. (In communication II comparisons with the bibliography and hygienic consequences will be published.)

Borneff, J., R. Hassinger, et al. (1988). "[The distribution of microorganisms in household kitchens. II. Evaluation of results and hygienic inferences]." Zentralbl Bakteriol Mikrobiol Hyg [B] 186(1): 30-44.
	The very high morbidity rates of Enteritis infectiosa diseases demand improved prophylactic measures. An important indication of the source of these illnesses is the fact that infections in private households are about three times more frequent than in canteens. Indeed, the rise in morbidity is undoubtedly caused by inadequate treatment of raw products, of meal rests and by insufficient heating processes. Furthermore, in household kitchens no efforts are made to interrupt infection chains, and disinfections are considered as superfluous and housewives are content if their kitchens appear to be clean. The aim of our study performed in a normal household kitchen, was to investigate cross-contamination caused by pathogens, introduced into the kitchen from outdoors. A further aim was to establish the main sources of contamination in order to be able to recommend practical disinfection procedures. The main fields of contamination discovered when 55 meals prepared were: a) working surfaces (including boards of wood and plastics) b) kitchen- and cutting-machines. The amount of test organisms (Sarcinae), introduced into the kitchen (unbeknown to the housewives) by experimentally contaminated minced meat was only reduced by common cleaning procedures, in sofar as nearly half of the original contaminations could be demonstrated to be still present. However, when the normal cleanser was replaced by one containing hypochlorite, and with retention of the same working routines, about 90% bacteriologically clean surfaces were determined. In this way it could be demonstrated that infection chains can be interrupted. It is, however, not correct to compare the efficiency of these procedures with the efficiency of disinfection, according to the Federal Infectious Diseases Act (Bundesseuchengesetz). On practical application of these experiences it must be borne in mind that housewives should not be forced to apply medical disinfection procedures: indeed, traditional and practised cleaning methods should be retained, as far as possible. We recommend therefore that manufacturers supply household cleansers with an anti-bacterial additive, after its application in the kitchens working surfaces and machines are bacteriologically clean. Additionally housewives should be appropriately informed about the necessity of these manipulations. We consider minimization of toxicity and a thorough environmental compatibility of formulations to be self-evident.

Borrego, J. J., R. Cornax, et al. (1991). "Development and application of new positively charged filters for recovery of bacteriophages from water." Appl Environ Microbiol 57(4): 1218-22.
	Electronegative and electropositive filters were compared for the recovery of indigenous bacteriophages from water samples, using the VIRADEL technique. Fiber glass and diatomaceous earth filters displayed low adsorption and recovery, but an important increase of the adsorption percentage was observed when the filters were treated with cationic polymers (about 99% adsorption). A new methodology of virus elution was developed in this study, consisting of the slow passage of the eluent through the filter, thus increasing the contact time between eluent and virus adsorbed on the filters. The use of this technique allows a maximum recovery of 71.2% compared with 46.7% phage recovery obtained by the standard elution procedure. High percentages (over 83%) of phage adsorption were obtained with different filters from 1-liter aliquots of the samples, except for Virosorb 1-MDS filters (between 1.6 and 32% phage adsorption). Phage recovery by using the slow passing of the eluent depended on the filter type, with recovery ranging between 1.6% for Virosorb 1-MDS filters treated with polyethyleneimine and 103.2% for diatomaceous earth filters treated with 0.1% Nalco.

Bosch, A. (1998). "Human enteric viruses in the water environment: a minireview." Int Microbiol 1(3): 191-6.
	Water virology started around half a century ago, with scientists attempting to detect poliovirus in water samples. Since that time, other enteric viruses responsible for gastroenteritis and hepatitis, among a great variety of virus strains, have replaced enteroviruses as the main target for detection in the water environment. Technical molecular developments, polymerase-chain reaction (PCR) amplification being the method of choice, enable the detection of fastidious health-significant viruses. However, shortcomings of molecular procedures include their potential incompatibility with concentration methods, indispensable to reduce the water sample volume to assay for viruses, the inability to discern between infectious and non infectious material. On the other hand, these procedures are restrained to sophisticated laboratories and detection of alternative indicator organisms has been proposed. Bacterial indicators fail to give a reliable clue of the virological quality of water. Selected bacteriophage groups appear as a better choice for their use as virus indicators.

Bosch, A., F. X. Abad, et al. (1994). "Should shellfish be purified before public consumption?" Lancet 344(8928): 1024-1025.
	
Bosch, A., R. Gajardo, et al. (1996). "Non isotopic automatable molecular procedures for the detection of enteroviruses." Mol Cell Probes 10(2): 81-9.
	Five microwell non isotopic hybridization assays, based on colorimetric immunoenzymatic reading, were developed and evaluated for the rapid and automatable detection of enteroviruses. Virus nucleic acids and/or capture probes were covalently bound to microtiter wells, and digoxigenin-11-dUTP was used as label for the detection of hybridized material. Among these procedures, a reverse transcriptase polymerase chain reaction (RT-PCR) hybridization assay was the most sensitive, enabling the detection of 10 MPNCU of poliovirus, and offering detection specificity for other enteroviruses, such as coxsackieviruses and echoviruses. The second most sensitive method was a complementary hybridization assay, simultaneously using three detection probes, one from the 5' end and two from the 3' end of poliovirus genome, offering a sensitivity for poliovirus detection of 5 x 10(3) MPNCU.

Bosch, A., J. F. Gonzalez-Dankaart, et al. (1998). "A new continuous epitope of hepatitis A virus." Journal of Medical Virology 54(2): 95-102.
	A new continuous epitope of hepatitis A virus (HAV) was defined in the VP3 protein. Convalescent sera recognised the synthetic peptide 3110- 3121 (FWRGDLVFDFQV). The replacement of the arginine, glycine, or aspartic acid at positions 112, 113, or 114, respectively by other amino acids induced the loss of synthetic peptide recognition by human convalescent sera, thereby confirming the presence of an epitope in the original VP3(110-121) sequence. Shorter VP3 peptides such as VP3(110- 119). VP3(110-117), and VP3(110-116) and a tandem repeat of VP3(111- 116) failed to react with convalescent sera, indicating the importance of the entire peptide in the epitope structure. The maximum inhibition of human convalescent binding to HAV by the VP3(110-121) peptide was around 60%, and 50% inhibition was achieved at a peptide concentration of 2.3-2.4 micrograms/ml. Antibodies generated by this peptide bound to intact HAV and neutralised its infectivity. Antipeptide antibodies inhibited convalescent serum binding to HAV. Monoclonal antibodies H7C27 and MAK-4E7 inhibited completely binding of the antipeptide antibodies to HAV.

Bosch, A., M. Gray, et al. (1993). "The survival of human enteric viruses in seawater." BIOGEOCHEMICAL CYCLES OF SPECIFIC POLLUTANTS (ACTIVITY K): SURVIVAL OF PATHOGENS. FINAL REPORTS OF RESEARCH PROJECT (1992-1993).#CYCLES BIOGEOCHIMIQUES DE POLLUANTS SPECIFIQUES (ACTIVITE K), SURVIE DES PATHOGENES. RAPPORTS FINAUX SUR LES PROFETS DE RECHERCHE (1992-1993)., UNEP.
	Human pathogenic viruses enter the marine environment primarily through the discharge of treated and untreated sewage into surface waters. Since current treatment practices do not provide virus-free effluents, enteric viruses are routinely discharged into estuarine and coastal waters. The critical question which arises, however, is whether or not these viruses can survive long enough and in high enough concentration to cause disease in individuals who are in contact with polluted recreational water or who consume contaminated seafood. The phenomenon that self purification processes are more pronounced in seawater than in river water has been reported by several authors. However, there appears to be no consensus on the nature of the factor(s) responsible for the virucidal capacity of seawater. Several observations demonstrate the potential involvement of native marine microorganisms in the inactivation of viruses in marine habitats, although data on the successful isolation of microorganisms with virucidal properties are scarce. Additionally, the ability of bacteria to inactivate viruses is usually lost while subculturing the bacteria in the laboratory. The present report deals with the effect of different types of seawater on the survival of human enteric viruses, and the influence of the presence of marine bacteria on the virucidal capacity of seawater.

Bosch, A., F. Lucena, et al. (1991). "Waterborne Viruses Associated with Hepatitis Outbreak." Journal of the American Water Works Association JAWWA5 83: No. 3, p 80-83, March 1991. 1 fig.
	Human enteric viruses were isolated from the potable water of a military camp in Spain that was experiencing an outbreak of infectious hepatitis, despite a total chlorine residual in the water of 0.2 mg/L. On February 1, 1988, during the peak of the infectious hepatitis cases, water samples were taken for physicochemical, bacteriological, and virological analysis from 9:45 a.m. to 6:45 p.m. Five untreated water samples were collected from the 120,000 L reservoir, while tap water was sampled from a camp faucet that had been allowed to flow for several minutes. The bacteriological analysis, a two-day incubation in trypticase soy agar at 30 C for a standard plate count, showed the water to be consistently free of indicator bacteria. Virological analyses were performed for the presence of enteroviruses, rotaviruses, and hepatitis A. The Valira River appears to be contaminated with human enteric viruses. The outbreak of illness at the camp may have been caused by the fecal contamination of the Valira River, which receives occasional wastewater discharges from Andorra, and the inadequacy of the processes used to treat the water. These results support monitoring of viral contamination and more powerful water treatment when viruses have been detected in the water supply. (Brunone-PTT)

Bosch, A., F. Lucena, et al. (1986). Fate of Human Enteric Viruses Rotaviruses and Enteroviruses in Sewage after Primary Sedimentation. 13th International Association on Water Pollution Research and Control Biennial Conference on Health-Related Water Microbiology, Rio De Janeiro, Brazil, August 20-22, 1986. Water Sci Technol.
	
Bosch, A., R. M. Pinto, et al. (1995). "Differential accumulation and depuration of human enteric viruses by mussels." Water Science & Technology 31, no. 5-6: 447-451.
	The tissue distribution of adenovirus 40 (ADV) and human rotavirus, serotype 3 (HRV) was determined after feeding the common mussel (Mytilus spp.) with high levels of clay-associated virus. At different time intervals, individual tissues were carefully dissected and assayed for infectivity. Viruses were detected in contaminated mussels after 1-hour contact, and maximum levels were observed after 6 hours. Most infectious viruses were located in the gills and in the digestive tract. Decreasing virus numbers were found in the mantle lobes. Mussels contaminated with poliovirus 1 (PV), hepatitis A virus, strain HM-175 (HAV), ADV, HRV, and bacteriophages of Bacteroides fragilis (B40-8) were depurated in 50-1 tanks with a continuous flow of ozonated marine water. After 96 hours, HAV and HRV suffered less than 2 Log sub(10) titre reduction (LTR), while ADV showed a 2.7 LTR. PV showed a 3 LTR after 48 hours and became undetectable thereafter. Bacteriophage B40-8 suffered less than 2 LTR after 96 hours, suggesting that it could be an appropriate indicator of the efficiency of virus elimination during shellfish depuration.

Bosch, A., R. M. Pinto, et al. (1997). "Persistence of human astrovirus in fresh and marine water." HEALTH-RELATED WATER MICROBIOLOGY 1996: 243-247.
	Large gastroenteritis outbreaks associated with astrovirus are being reported with increasing frequency suggesting that astrovirus may be an important agent of epidemic acute non-bacterial gastroenteritis in children and adults. In this study, a procedure, based on infection of CaCo-2 cell monolayers followed by reverse-transcription polymerase chain reaction, was developed to ascertain the persistence of infectious human astroviruses in tap and marine water at 4 plus or minus 1 degree C and 20 plus or minus 1 degree C. The adequacy of this methodology for monitoring the decay of infectious fastidious viruses was assessed by determining the survival of a cytocidal virus (poliovirus 1) concomitantly by MPNCU and cell infection plus RT-PCR. After 60d in dechlorinated tap water, the decay of astrovirus infectivity was lower than 2 logs at 4 plus or minus 1 degree C and around 3.6 logs at 20 plus or minus 1 degree C, while after 90 d the titre reduction was around 3.3 and 4.3 logs at 4 plus or minus 1 degree C and 20 plus or minus 1 degree C respectively. In natural non-autoclaved seawater at 20 degree C, astrovirus showed a lower level of persistence. The possibility to acquire data on the survival of fastidious viruses in the environment opens new perspectives on the epidemiology of some health significant infections transmitted by the faecal-oral route.

Bosch, A., G. Sanchez, et al. (2001). "Human enteric viruses in Coquina clams associated with a large hepatitis A outbreak." Water Sci Technol 43(12): 61-5.
	An outbreak of hepatitis A, affecting 183 people, occurred in Valencia (Spain). Epidemiological evidence pointed to an association of the outbreak with consumption of Coquina clams (Donax sp), imported frozen from Peru. Shellfish were analysed for the presence of hepatitis A virus (HAV), enteroviruses, rotaviruses, astroviruses, caliciviruses and hepatitis E virus. HAV was detected in 75% of assayed shellfish samples. Other enteric viruses were occasionally found in the same samples. Molecular epidemiological analysis of fragments of the VP1/2A and the 5' end of the genome from shellfish and sera isolates, revealed the presence of six variants belonging to a single genotype.

Boshuizen, J. A., J. H. Reimerink, et al. (2003). "Changes in small intestinal homeostasis, morphology, and gene expression during rotavirus infection of infant mice." J Virol 77(24): 13005-16.
	Rotavirus is the most important cause of infantile gastroenteritis. Since in vivo mucosal responses to a rotavirus infection thus far have not been extensively studied, we related viral replication in the murine small intestine to alterations in mucosal structure, epithelial cell homeostasis, cellular kinetics, and differentiation. Seven-day-old suckling BALB/c mice were inoculated with 2 x 10(4) focus-forming units of murine rotavirus and were compared to mock-infected controls. Diarrheal illness and viral shedding were recorded, and small intestinal tissue was evaluated for rotavirus (NSP4 and structural proteins)- and enterocyte-specific (lactase, SGLT1, and L-FABP) mRNA and protein expression. Morphology, apoptosis, proliferation, and migration were evaluated (immuno)histochemically. Diarrhea was observed from days 1 to 5 postinfection, and viral shedding was observed from days 1 to 10. Two peaks of rotavirus replication were observed at 1 and 4 days postinfection. Histological changes were characterized by the accumulation of vacuolated enterocytes. Strikingly, the number of vacuolated cells exceeded the number of cells in which viral replication was detectable. Apoptosis and proliferation were increased from days 1 to 7, resulting in villous atrophy. Epithelial cell turnover was significantly higher (<4 days) than that observed in controls (7 days). Since epithelial renewal occurred within 4 days, the second peak of viral replication was most likely caused by infection of newly synthesized cells. Expression of enterocyte-specific genes was downregulated in infected cells at mRNA and protein levels starting as early as 6 h after infection. In conclusion, we show for the first time that rotavirus infection induces apoptosis in vivo, an increase in epithelial cell turnover, and a shutoff of gene expression in enterocytes showing viral replication. The shutoff of enterocyte-specific gene expression, together with the loss of mature enterocytes through apoptosis and the replacement of these cells by less differentiated dividing cells, likely leads to a defective absorptive function of the intestinal epithelium, which contributes to rotavirus pathogenesis.

Bosque, P. J., C. Ryou, et al. (2002). "Prions in skeletal muscle." Proc Natl Acad Sci U S A 99(6): 3812-7.
	Considerable evidence argues that consumption of beef products from cattle infected with bovine spongiform encephalopathy (BSE) prions causes new variant Creutzfeldt-Jakob disease. In an effort to prevent new variant Creutzfeldt-Jakob disease, certain "specified offals," including neural and lymphatic tissues, thought to contain high titers of prions have been excluded from foods destined for human consumption [Phillips, N. A., Bridgeman, J. & Ferguson-Smith, M. (2000) in The BSE Inquiry (Stationery Office, London), Vol. 6, pp. 413-451]. Here we report that mouse skeletal muscle can propagate prions and accumulate substantial titers of these pathogens. We found both high prion titers and the disease-causing isoform of the prion protein (PrP(Sc)) in the skeletal muscle of wild-type mice inoculated with either the Me7 or Rocky Mountain Laboratory strain of murine prions. Particular muscles accumulated distinct levels of PrP(Sc), with the highest levels observed in muscle from the hind limb. To determine whether prions are produced or merely accumulate intramuscularly, we established transgenic mice expressing either mouse or Syrian hamster PrP exclusively in muscle. Inoculating these mice intramuscularly with prions resulted in the formation of high titers of nascent prions in muscle. In contrast, inoculating mice in which PrP expression was targeted to hepatocytes resulted in low prion titers. Our data demonstrate that factors in addition to the amount of PrP expressed determine the tropism of prions for certain tissues. That some muscles are intrinsically capable of accumulating substantial titers of prions is of particular concern. Because significant dietary exposure to prions might occur through the consumption of meat, even if it is largely free of neural and lymphatic tissue, a comprehensive effort to map the distribution of prions in the muscle of infected livestock is needed. Furthermore, muscle may provide a readily biopsied tissue from which to diagnose prion disease in asymptomatic animals and even humans.

Bostock, A. D., P. Mepham, et al. (1979). "Hepatitis A infection associated with the consumption of mussels." Journal of Infection 1: 171-177.
	
Botero, L., M. Montiel, et al. (1996). "Enteroviruses in shrimp harvested from contaminated marine waters." International Journal of Environmental Health Research 6(2): 103-108.
	Marine shrimp (genus Penaeus) live primarily in tropical and subtropical coastal locations, sometimes contaminated by domestic sewage. However, sanitary quality and importance of shrimp as a potential vehicle for enteric disease transmission have not been reported previously. The shrimp Penaeus schmitti were either collected directly from Lake Maracaibo, in western Venezuela, or obtained from local seafood outlets. Of a total of 33 pooled samples, 16 (49%) yielded virus. Six types of enteroviruses were isolated during this study: polioviruses 1 and 2, and echovirus types 20, 21, 27, and 29. Viruses not typeable with the pools of specific antiserum used during this study were isolated from seven samples. Analysis of the results indicate that enteroviruses may be present in shrimp populations present in sewage-contaminated marine and estuarine waters.

Bothner, B. and G. Siuzdak (2004). "Electrospray ionization of a whole virus: analyzing mass, structure, and viability." Chembiochem 5(3): 258-60.
	
Botic, T., T. D. Klingberg, et al. (2007). "A novel eukaryotic cell culture model to study antiviral activity of potential probiotic bacteria." Int. J. Food Microbiol. 115(2): 227-234.
	As shown in many intervention studies, probiotic bacteria can have a beneficial effect on rotavirus and HIV-induced diarrhoea. In spite of that fact, antiviral effects of probiotic bacteria have not been systematically studied yet. Non-tumorigenic porcine intestinal epithelial cells (IPEC-J2) and alveolar macrophages (3D4/2) were treated in different experimental designs with probiotic and other lactic bacteria and their metabolic products. Vesicular stomatitis virus (VSV) was used in the study as a model virus. Cell survival and viral inhibition were determined by antiviral assay and confirmed by immunofluorescence. Pre-incubation of cell monolayers with probiotic bacteria reduced viral infectivity up to 60%. All bacteria used prevented VSV binding to the cell monolayers by direct binding of VSV to their surface. Probiotic and other lactic bacteria prevented viral infection also by establishment of the antiviral state in pre-treated cell monolayers. Probiotic and other lactic bacteria secreted antiviral substances during their growth, as the infectivity of the virus was diminished by 68% when bacterial supernatants were tested. It was shown for the first time that probiotic and other lactic bacteria exhibit an antiviral activity in a cell culture model. Possible mechanisms of antiviral activity include: 1) hindering the adsorption and cell internalisation of the VSV due to the direct trapping of the virus by the bacteria, 2) "cross-talk" with the cells in establishing the antiviral protection and 3) production of metabolites with a direct antiviral effect.

Bottiger, M. (1987). "A study of the sero-immunity that has protected the Swedish population against poliomyelitis for 25 years." Scand J Infect Dis 19(6): 595-601.
	Although the population was highly susceptible to poliomyelitis on account of its low natural immunity, the general vaccination with inactivated polio vaccine eliminated poliomyelitis in Sweden within 6 years (1957-62). This status remains after 25 years, although challenges from the introduction of virus occur constantly. Over 99% of the population born in the forties and later is estimated to have been vaccinated, as well as at least 90% of those born earlier. The mean antibody levels of vaccinees against polio range from 100 (type 3) and 500 (type 1) up to 800 (type 2). Seronegative persons are seen only in a small percentage. Evaluation of the duration of immunity indicates that, after the post-vaccination fall in titre which occurs within 2-5 years after immunization, the immune levels remain fairly stable or decline very slowly. Sera from 12-year-old Swedish vaccinees neutralized the type 3 Saukett strain used for vaccine production 5 times better than a type 3 strain isolated during the Finnish outbreak 1984.

Bottiger, M., B. Christenson, et al. (1997). "Hepatitis A immunity in the Swedish population. A study of the prevalence of markers in the Swedish population." Scand J Infect Dis 29(2): 99-102.
	After a 20-year interval, the prevalence of seroimmunity to Hepatitis A (HA) was again investigated in a statistical sample of the adult Swedish population. Sera from 3382 of the 4800 originally selected persons were tested. The prevalence of antibodies to HA had not changed since the 1960s when only the Scandinavian population was considered. In the oldest population born at the beginning of this century, the presence of antibodies amounted to 69%. It gradually declined to 6% in those born in the 1940s. In the population born after 1950, the percentage of seropositive individuals was only 2%. A slightly higher prevalence was seen in the big cities, compared with the rural areas (13% vs 9%). Persons of non-Scandinavian origin showed a different pattern. Those from other European countries showed a prevalence of about 70% in all the age-groups investigated. Among the young adults of Arabic or Asiatic origin, the figure was > 90%. The conclusion is that the native Swedish population has a low natural exposure to HA, which has not changed during the last 20 years. Prophylaxis before going to countries where the disease is endemic is strongly recommended.

Bottiger, M. and E. Herrstrom (1992). "Isolation of polioviruses from sewage and their characteristics: experience over two decades in Sweden." Scand J Infect Dis 24(2): 151-5.
	Indigenous polio ceased in Sweden in 1962 after 5 years' use of killed polio vaccine. In 1967, it was considered of interest to investigate whether poliovirus was present in the sewage. A method for selective isolation of poliovirus from sewage was developed. The method appeared to increase the yield. The studies were carried out at intervals up to 1990. In 1989-90, the virus isolates were characterized by the use of monoclonal antibodies differentiating between vaccine-like (Sabin-like) and non-vaccine-like strains. Polioviruses of both kinds were isolated throughout the period. Two periods were of special interest. The first was in 1977, when a single, paralytic, type-2 case occurred in Sweden in an unvaccinated sect. The second was in 1984-85 when a type-3 epidemic broke out in Finland, followed by vaccinations of the whole Finnish population with live oral polio vaccine. On both occasions the implicated viruses could be traced to a high degree in sewage in Sweden. The absence of poliovirus isolations from faecal specimens of patients and the isolation of live poliovirus vaccine virus, i.e. a vaccine not used in Sweden, indicate that the virus strains are imported.

Bouchriti, N. and S. M. Goyal (1992). "Evaluation of three methods for the concentration of poliovirus from oysters." Microbiologica 15(4): 403-408 
	Three methods for the concentration of poliovirus from oyster homogenates were compared. The adsorption-elution-precipitation method gave the lowest average virus recovery (24.1%), while the beef extract elution-acid precipitation method and the non-fat dry milk elution-acid precipitation methods gave recoveries of 47.2% and 39.6%, respectively. Although the overall recovery rates with these methods were lower than those reported in previous studies, recoveries of 40-47% obtained with the elution-precipitation methods used in the present study are considered to be above average in terms of recovery efficiency. 

Bouchriti, N. and S. M. Goyal (1993). "Methods for the concentration and detection of human enteric viruses in shellfish: a review." Microbiologica 16(1): 105-114.
	(Summary) Shellfish, including oysters, mussels, and clams, are filter feeding bivalve mollusks and can accumulate human pathogens at levels higher than those in their surrounding waters. Outbreaks of shellfish-borne enteric viral diseases have been reported worldwide. To determine the public health safety of shellfish, methods are available for the direct detection of human enteric viruses in shellfish tissues. Potential problems with these methods include (i) toxicity of the final sample to cell cultures used for viral assay, and (ii) a large sample volume that cannot be conveniently assayed. To overcome these problems, several methods for the concentration and detection of enteric viruses in shellfish tissues have been developed and utilized. A review of these methods indicates that none of them is universally accepted because no single method is equally effective for shellfish obtained from different geographical locations and under all conditions. It is suggested, therefore, that a proposed method should first be tested under experimental conditions, utilizing virus-spiked shellfish, before using it under field conditions. 

Bouchriti, N., S. M. Goyal, et al. (1994). "Comparison of three methods for the concentration of poliovirus from Moroccan shellfish." Journal of Food Protection 57(11): 996-1000.
	Three methods were evaluated for the concentration of poliovirus from artificially contaminated oysters (Crassostrea gigas), mussels (Mytilus edulis) and carpet-shell clams (Ruditapes decussatus) grown in Morocco. The methods tested were: an adsorption-elution-precipitation method, a beef extract elution acid-precipitation method, and a non-fat dry milk elution acid-precipitation method. For all shellfish species tested, the adsorption-elution-precipitation method yielded the lowest average virus recovery (27%), whereas the two elution-precipitation methods yielded average virus recoveries of 42% each. The beef extract elution acid-precipitation method yielded the highest virus recovery with clams (53%), whereas non-fat dry milk elution acid-precipitation was advantageous for mussels providing average virus recovery of 47%. For oysters, none of the tested methods gave satisfactory virus recovery. These results point towards the need for the development of better method(s) for the concentration of viruses from Moroccan oysters, while for mussels and clams, the elution-acid precipitation methods may be satisfactory.

Bounlu, K., S. Insisiengmay, et al. (1998). "Acute jaundice in Vientiane, Lao People's Democratic Republic." Clin Infect Dis 27(4): 717-21.
	Analysis of serum samples from patients with acute jaundice by means of enzyme-linked immunosorbent assay and polymerase chain reaction testing provided the first profile of this condition in Vientiane, Lao PDR, in 1995 and 1996. In a case-control, hospital-based study, evidence of acute infections due to hepatitis A and B viruses was found in 14% and 10% of cases, respectively. Hepatitis E virus, however, did not appear to contribute to clinically recognized acute jaundice. Similarly, antibody to hepatitis C virus was recognized in almost equal proportions of cases (8%) and controls (6%), thus representing probable background infections. The detection of hepatitis G virus marks the first report of this virus in Lao PDR. The large proportion (21%) of new leptospiral infections in cases without acute hepatitis A or B was notable. This finding suggests significant regional underreporting of leptospirosis as a cause of acute jaundice. The limited laboratory diagnostic capabilities for confirming a differential diagnosis of leptospirosis contribute to the lack of attention paid to this important health problem.

Boxman, I. L., J. J. Tilburg, et al. (2007). "An efficient and rapid method for recovery of norovirus from food associated with outbreaks of gastroenteritis." J. Food Prot. 70(2): 504-508.
	Noroviruses have emerged as the most common cause of foodborne outbreaks of acute nonbacterial gastroenteritis. In this study, two methods for the extraction of viruses from deli ham were compared. Using both methods, as little as 1 to 10 reverse transcription (RT)-PCR units of inoculated norovirus and enterovirus could be detected by nested RT-PCR assays. The fastest and most efficient extraction method based on TRIzol LS Reagent was chosen to identify viruses in food items associated with three different outbreaks. Norovirus was detected using nested (real time) RT-PCR assays that target the genome region routinely used for diagnosis of human cases, thereby facilitating the comparison of sequences detected in food and clinical specimens. For one outbreak, a norovirus sequence (163/163 nucleotides) identical to those detected in clinical samples was found on salami sliced by a food handler with a recent history of gastroenteritis. For the other two outbreaks, norovirus was detected on leftovers of spareribs and ham, but fecal samples from affected persons were not available. The methods used in this study may be useful in future outbreak investigations because the extraction method is easy to perform and suitable for this particular type of food and the detection method facilitates direct comparison of patient and food data.

Boxman, I. L., J. J. Tilburg, et al. (2006). "Detection of noroviruses in shellfish in the Netherlands." Int J Food Microbiol 108(3): 391-6.
	Shellfish from oyster farms in the Netherlands and imported from other European countries were examined for viral contamination. A method that allows sequence matching between noroviruses from human cases and shellfish was used. The samples of shellfish (n = 42) were analyzed using a semi-nested RT-PCR that had been optimized for detection of norovirus in shellfish (SR primer sets). In addition, a different genome region was targeted using a second primer set which is routinely used for diagnosis of norovirus infection in humans (JV12Y/JV13I). To improve the detection limit for this RT-PCR a semi-nested test format was developed (NV primer sets). One of 21 oyster samples (4.8%) from Dutch farms was norovirus positive, whereas norovirus was detected in 1 out of 8 oyster samples (12.5%) and 5 out of 13 mussel samples (38.5%) collected directly after importation in the Netherlands. RNA from samples associated with an outbreak of gastro-enteritis in the Netherlands in 2001 was re-analyzed using the NV primer sets. At least one identical sequence (142/142 nt) was found in three fecal and in two oyster samples related to this outbreak. Further surveillance of norovirus by detection and typing of viruses from patients with gastroenteritis and shellfish is warranted to clarify the causes of future outbreaks.

Brack, K., I. Berk, et al. (2002). "Hepatitis A virus inhibits cellular antiviral defense mechanisms induced by double-stranded RNA." J Virol 76(23): 11920-30.
	The consequences of a hepatitis A virus (HAV) infection on cell-based antiviral responses and the interactions between virus and host cells resulting in persistent infections are poorly understood. In this report, we show that HAV does inhibit double-stranded (dsRNA)-induced beta interferon (IFN-beta) gene expression by influencing the IFN-beta enhanceosome, as well as dsRNA-induced apoptosis, which suggests that both effects may be connected by shared viral and/or cellular factors. This ability of HAV, which preserves the sites of virus production for a longer time, may allow the virus to establish an infection and may be the presupposition for setting up persistent infections. Our results suggest that the inhibitory effect of HAV on the cellular defense mechanisms might not be sufficient to completely prevent the antiviral reactions, which may be induced by accumulating viral dsRNA, at a later stage of infection. However, HAV seems to counteract this situation by downregulation of viral replication and in the following production of viral dsRNA. This ability of noncytopathogenic HAV acts dominantly on cytopathogenic HAV in trans. The downregulation might ensure the moderate replication which seems necessary for inhibition of the antiviral mechanisms by HAV and therefore for the persistent state of the HAV infection.

Brack, K., W. Frings, et al. (1998). "A cytopathogenic, apoptosis-inducing variant of hepatitis A virus." J. Virol. 72(4): 3370-3376.
	A cytopathogenic variant of hepatitis A virus (HAV(cyt/HB1.1)) was isolated from persistently infected BS-C-1 cells by serial passages in FRhK-4 cells. This virus shows a rapid replication pattern and high final titers are obtained, which are main characteristics of cytopathogenic HAVs. Sequencing of the nontranslated regions and the coding regions for 2ABC and 3AB revealed that mutations are distributed all over these regions and that certain mutated sites correspond to those in other cytopathogenic HAV variants. Investigating the mechanisms causing the cytopathic effect in FRhK-4 cells infected with this variant, we found that an apoptotic reaction takes place.

Bradley, D., A. Andjaparidze, et al. (1988). "Aetiological agent of enterically transmitted non-A, non-B hepatitis." J. Gen. Virol. 69 ( Pt 3): 731-738.
	Virus-like particles (VLPs) with a mean diameter of 32 nm were recovered from the stools of three acute phase cases of enterically transmitted non-A, non-B hepatitis (ET-NANBH) occurring in the Soviet Union, North Africa and North America. VLPs from two of these cases were studied in detail and were shown to react specifically with antibody in acute phase sera obtained from other cases of ET-NANBH in Asia, the Soviet Union, North Africa and North America. Partially purified VLPs were found to sediment at 183S in sucrose gradients and to cross-react with antibody in acute phase sera from geographically isolated cases of ET-NANBH. The latter virus preparations were also used to document the seroconversion of experimentally ET-NANBH-infected cynomolgus macaques to 32 nm VLPs. Our findings indicate that one virus or class of viruses is responsible for the majority of ET-NANBH.

Bradley, D. W. (1995). "Hepatitis E virus: a brief review of the biology, molecular virology, and immunology of a novel virus." J Hepatol 22(1 Suppl): 140-5.
	Our basic understanding of the biology, molecular virology, and immunology of hepatitis E virus (HEV) is briefly reviewed. HEV is a small, round, nonenveloped virus with morphologic and biophysical properties most similar to viruses found in the family Caliciviridae. The genome of HEV is approximately 7.5 kb in length and consists of a positive-sense, single-stranded RNA molecule that contains three distinct open reading frames (ORF1, ORF2, ORF3) that appear to encode for nonstructural and structural proteins based on the presence of well-defined consensus motifs and genomic organization similar to those of other calici- or calici-like viruses. Limited epitope mapping of the viral genome with synthetic peptides has revealed the presence of highly immunoreactive type-common and type-specific epitopes; these finding are consistent with the results of other studies that used recombinant expressed proteins from both the nonstructural and structural regions of the derived viral proteins encoded by ORFs 1, 2, and 3. Synthetic peptides and recombinant expressed proteins have been used to develop Western blot assays and enzyme immunoassays (EIAs) for the detection of IgA, IgG, and IgM anti-HEV in human and primate sera. Knowledge of the dynamics of HEV antigen and antibody expression in experimentally-infected primates is emerging, and prototype vaccines have been developed with recombinant expressed ORF2 and ORF3 proteins. Limited seroprevalence studies of anti-HEV in endemic and nonendemic regions of the world using one or more of the above assays has revealed a strong correlation between level of sanitation and incidence of disease and prevalence of anti-HEV.

Bradley, D. W. and M. S. Balayan (1988). "Virus of enterically transmitted non-A, non-B hepatitis." Lancet 1(8589): 819.
	
Bradley, D. W., K. Krawczynski, et al. (1987). "Enterically transmitted non-A, non-B hepatitis: serial passage of disease in cynomolgus macaques and tamarins and recovery of disease-associated 27- to 34-nm viruslike particles." Proc Natl Acad Sci U S A 84(17): 6277-81.
	An experimental model of enterically transmitted non-A, non-B hepatitis (ET-NANBH) was established in tamarins (Saguinus mystax mystax) and cynomolgus macaques (Macaca fascicularis). First-passage animals were inoculated with two different stool suspensions obtained from human patients with well-defined ET-NANBH that originated from Burma and Pakistan, where epidemics of ET-NANBH occur. Both inocula contained 27- ato 34-nm-diameter viruslike particles (VLPs) that were specifically aggregated by acute-phase ET-NANBH sera. ET-NANBH was subpassaged in both tamarins and cynomolgus macaques by using pools of stool suspensions from first-passage animals. One additional passage of disease in cynomolgus macaques resulted in a significantly shortened incubation period and increased severity of disease. VLPs similar to those found in the human inocula were observed in stool specimens of first-, second-, and third-passage cynomolgus macaques and in first- and second-passage tamarins. Our findings indicate that cynomolgus macaques are particularly suitable experimental models for studies of human ET-NANBH. The 27- to 34-nm VLPs found in infected human and primate stools appear to be etiologically linked to disease.

Bradley, D. W., K. A. McCaustland, et al. (1982). "Dissociation of hepatitis A virus antigen-anti-HAV antibody complexes by 2-mercaptoethanol and dithiothreitol." J Med Virol 9(4): 311-25.
	Intravenous inoculation of two marmosets and one chimpanzee with hepatitis A virus (HAV) resulted in the replication of virus in liver, excretion of HAV particles in stool, and the appearance of circulating antibodies specific for hepatitis A. The development of an early antibody response in the chimpanzee and in one of the two infected marmosets was shown to interfere with the serologic detection of HAV antigen (HAV Ag) in homogenates of acute phase liver tissue obtained from these animals. Treatment of HAV Ag-positive and IgM anti-HAV-positive liver homogenates with thiol reducing compounds was shown to release HAV Ag from in vitro formed immune complexes. The increased RIA response for HAV Ag in homogenates treated with 2-mercaptoethanol (2-ME) or dithiothreitol (DTT) was further shown not to be due to activation of HAV Ag itself or to a nonspecific effect on the RIA coating antibody, radiolabeled probe, or homogenized liver tissue. IgG and IgM double-antibody sandwich RIAs for HAV Ag were also compared for their ability to detect HAV Ag under reducing and nonreducing conditions. Application of the 2-ME or DTT treatment procedure to the serologic detection of other viral antigens or viruses whose presence in blood, stool, tissue macerate, or other milieu may be masked by specific antibody appears to be feasible.

Brandner, S., M. A. Klein, et al. (2000). "Neuroinvasion of prions: insights from mouse models." Exp Physiol 85(6): 705-12.
	The prion was defined by Stanley B. Prusiner as the infectious agent that causes transmissible spongiform encephalopathies. A pathological protein accumulating in the brain of scrapie-infected hamsters was isolated in 1982 and termed prion protein (PrPSc). Its cognate gene Prnp was identified more than a decade ago by Charles Weissmann, and shown to encode the host protein PrP(C). Since the latter discovery, transgenic mice have contributed many important insights into the field of prion biology, including the understanding of the molecular basis of the species barrier for prions. By disrupting the Prnp gene, it was shown that an organism that lacks PrP(C) is resistant to infection by prions. Introduction of mutant PrP genes into PrP-deficient mice was used to investigate the structure-activity relationship of the PrP gene with regard to scrapie susceptibility. Ectopic expression of PrP in PrP knockout mice proved a useful tool for the identification of host cells competent for prion replication. Finally, the availability of PrP knockout mice and transgenic mice overexpressing PrP allows selective reconstitution experiments aimed at expressing PrP in neurografts or in specific populations of haemato- and lymphopoietic cells. The latter studies have allowed us to clarify some of the mechanisms of prion spread and disease pathogenesis.

Branovic, K., D. Forcic, et al. (2003). "Application of short monolithic columns for improved detection of viruses." J Virol Methods 110(2): 163-71.
	Monolithic chromatography media represent a novel generation of stationary phases introduced in the last 10-15 years providing a chromatography matrix with enhanced mass transfer and hydrodynamic properties. These features allow for an efficient and fast separation of especially large biomolecules like e.g., DNA and viruses. In this study, the enrichment of virus RNA on short monolithic columns prior to molecular detection of viruses is described. Measles and mumps viruses were chosen as model viruses. The results show that it is possible to bind viral RNA on monoliths and concentrate viral nucleic acids from a fairly dilute sample. Consequently, a potential application of short monolithic columns is the concentration of virus RNA to improve the sensitivity and selectivity of viral detection with the possibility of isolating viral RNA from cell-free biological fluids.

Brashear, D. A. and R. L. Ward (1982). "Comparison of methods for recovering indigenous viruses from raw wastewater sludge." Appl Environ Microbiol 43(6): 1413-8.
	Five general methods for recovering indigenous viruses from raw wastewater sludge were compared. Each method included elution, concentration, and disinfection steps. The elution method, found to consistently yield the greatest viral recovery, was a two-phase technique that involved blending sludge with Freon. Other methods, including two being tested as American Society for Testing Materials tentative standard methods, were less effective. Viral recoveries were generally greater (sometimes much greater) if samples were concentrated by high-speed centrifugation rather than by organic flocculation with 3% beef extract. Three cell lines were used to measure viral recoveries by the plaque assay. The efficiency of recovery was greatest on BGM cells, followed by RD and MA-104 cells.

Brashear, D. A. and R. L. Ward (1983). "Inactivation of indigenous viruses in raw sludge by air drying." Appl Environ Microbiol 45(6): 1943-5.
	
Brassard, J., K. Seyer, et al. (2005). "Concentration and detection of hepatitis A virus and rotavirus in spring water samples by reverse transcription-PCR." J Virol Methods 123(2): 163-9.
	Every year, enteric viruses such as hepatitis A virus (HAV), rotaviruses, and noroviruses are responsible for viral gastro-enteritis and hepatitis reported worldwide. These viruses are mostly transmitted via the faecal-oral route, from direct contact between people, or by ingestion of contaminated food and water. Since only a few viral particles may cause disease, detection of low concentration of these viruses in food matrices is usually complex. The development of methods to concentrate viruses from food matrices is crucial in collecting data for the development of control strategies or for diagnostic purposes. In the present study, samples of bottled spring water were inoculated with known amounts of HAV (strain HM-175), and rotaviruses (strain Wa) viral particles and filtered through positively charged membranes. Elution of viruses attached to the membranes was achieved with a tryptose phosphate broth-glycine buffer. Eluates were further concentrated using Microsep 100. Finally, RNA was extracted using the Qiagen RNeasy kit followed by an evaporation step with a SpeedVac instrument. The detection limit by reverse-transcription (RT-PCR) was at least 10(-1) TCID50%/ml and at least 10(-3) TCID50%/ml for HAV and rotavirus, respectively.

Bratu, D. P., B. J. Cha, et al. (2003). "Visualizing the distribution and transport of mRNAs in living cells." Proc Natl Acad Sci U S A 100(23): 13308-13.
	We have visualized the movements of native mRNAs in living cells. Using nuclease-resistant molecular beacons, we imaged the transport and localization of oskar mRNA in Drosophila melanogaster oocytes. When the localization pattern was altered by genetic manipulation of the mRNA's 3' untranslated region, or by chemical perturbation of the intracellular tubulin network, the distribution of the fluorescence signals changed accordingly. We tracked the migration of oskar mRNA in real time, from the nurse cells where it is produced to the posterior cortex of the oocyte where it is localized. Our observations reveal the presence of a transient, and heretofore elusive, stage in the transport of oskar mRNA. Direct visualization of specific mRNAs in living cells with molecular beacons will accelerate studies of intracellular RNA trafficking and localization, just as the use of green fluorescent protein has stimulated the study of specific proteins in vivo.

Breindl, M. (1971). "The structure of heated poliovirus particles." J. Gen. Virol. 11(3): 147-156.
	
Breindl, M. (1971). "VP4, the D-reactive part of poliovirus." Virology 46(3): 962-964.
	
Breindl, M. and G. Koch (1972). "Competence of suspended HeLa cells for infection by inactivated poliovirus particles and by isolated viral RNA." Virology 48(1): 136-144.
	
Bresee, J. S., M. A. Widdowson, et al. (2002). "Foodborne viral gastroenteritis: challenges and opportunities." Clin Infect Dis 35(6): 748-53.
	Norwalk-like viruses (NLVs) are estimated to be the most common causes of foodborne disease in the United States, accounting for two-thirds of all food-related illnesses. The epidemiologic features and disease burden associated with NLVs have, until recently, been poorly understood because of the lack of sensitive detection assays and the underuse of available diagnostic tools. However, the application of molecular techniques to diagnose and investigate outbreaks of infection during recent years has led to a growing appreciation of the importance of these agents. NLVs are a principal cause of outbreaks of acute-onset vomiting and diarrhea in all age groups-most commonly, via contamination of uncooked foods by infected foodhandlers, but also via foods contaminated at their sources, such as oysters and raspberries. NLVs may also account for >10% of sporadic cases of gastroenteritis in children and adults. Future research will focus on the development of easy-to-use diagnostic assays based on antigen and antibody detection as well as vaccine development. Implementation of simple prevention measures, including correct food-handling practices, will continue to be a priority.

Bricout, F. (1992). "Viral diarrhorea." Presse Medicalf 21(7): 309-314.
	It is now well known that several viruses are responsible for acute diarrhoea or gastroenteritis in both children and adults. These viruses are difficult to identify since most of them cannot be isolated by stool cultures on cells. The reality of proven reinfection by some of these organisms is not always clearly understood, even though the existence of several serotypes in the same group (notably rotavirus) can be blamed, and this explains why vaccines are difficult to develop. 

Bridger, J. C. (1980). "Detection by electron microscopy of caliciviruses, astroviruses and rotavirus-like particles in the faeces of piglets with diarrhoea." Vet Rec 107(23): 532-3.
	
Brigati, D. J., D. Myerson, et al. (1983). "Detection of viral genomes in cultured cells and paraffin-embedded tissue sections using biotin-labeled hybridization probes." Virology 126(1): 32-50.
	A method of in situ cytohybridization is described for the detection of specific viral genomes in infected cell cultures or paraffin-embedded tissue sections without the use of radioisotopes. Biotin-labeled analogs of TTP are incorporated into viral DNA in vitro by nick translation and the resultant DNA probes hybridized to cytologic samples. Cells containing viral genetic material are then revealed by standard immunofluorescence, immunoperoxidase, or affinity cytochemical techniques that are based on the specific interaction between biotin and antibiotin IgG or avidin. Hybridization probes containing nucleotides that have an 11- or 16-atom spacer arm between the biotin molecule and the pyrimidine ring interact with these detector proteins more efficiently than probes containing biotin-nucleotides with a 4-atom spacer arm. The total procedure can be performed fairly rapidly (24 hr or less) and numerous samples can be processed simultaneously. Although the detection methods employed to date are not as sensitive as autoradiographic procedures with high specific activity probes, more sensitive protein detector complexes are currently being constructed. The speed, specificity, and resolving power of this technique should be of general utility in screening for the presence of infectious agents in cell or tissue samples. Here we report the visualization of parvovirus, polyomavirus, herpes simplex virus, adenovirus, and retrovirus genetic material in infected cell cultures and herpes simplex and adenovirus DNA in paraffin-embedded autopsy tissues. 

Brinker, J. P., N. R. Blacklow, et al. (1998). "Detection of Norwalk virus and other genogroup 1 human caliciviruses by a monoclonal antibody, recombinant-antigen-based immunoglobulin M capture enzyme immunoassay." J Clin Microbiol 36(4): 1064-9.
	Sera obtained from two groups of adult volunteers infected with Norwalk virus (NV) and two groups of patients involved in two natural outbreaks were tested for NV-reactive immunoglobulin M (IgM) by use of a monoclonal antibody, recombinant-antigen-based IgM capture enzyme immunoassay (EIA). No NV-reactive IgM was detected in the preinoculation sera of 15 volunteers, and 14 of 15 showed NV-reactive antibodies postinfection with NV. All of the volunteers showed IgG seroconversion to NV. In the outbreak studies, all 9 persons in one outbreak and 19 of 24 in another outbreak had NV-reactive IgM. In the first outbreak, only three of nine seroconverted to NV, which was likely due to late collection of acute-phase sera. In the second outbreak, 21 of 24 showed IgG seroconversion to NV. Sequencing of viruses isolated from five stool samples selected from those in the second outbreak showed that they were human calicivirus (HuCV) genogroup 1 viruses related, but not identical, to NV. In the volunteer studies, NV-reactive IgM was first detected 8 days postinoculation. The time of development of NV-reactive IgM antibodies in natural outbreaks was estimated to be similar to that found in the volunteer studies. Sera from three Hawaii virus-infected volunteers, four Snow Mountain virus patients, and 80 healthy individuals were negative for NV-reactive IgM, indicating test specificity for HuCV genogroup I infections. This capture IgM EIA is suitable for diagnosis of NV and other HuCV genogroup I infections and is especially useful when sera and fecal samples have not been collected early in the course of an outbreak.

Brinker, J. P., N. R. Blacklow, et al. (1999). "Immunoglobulin M antibody test to detect genogroup II Norwalk-like virus infection." J Clin Microbiol 37(9): 2983-6.
	Sera obtained from adult volunteers inoculated with genogroup II Norwalk-like viruses (NLVs), Hawaii virus, and Snow Mountain virus and from patients involved in outbreaks of gastroenteritis were tested for genogroup II NLV Mexico virus-specific immunoglobulin M (IgM) by use of a monoclonal antibody, recombinant Mexico virus antigen (rMXV)-based IgM capture enzyme-linked immunosorbent assay (ELISA). Sera from genogroup I Norwalk virus (NV)-inoculated volunteers and from patients involved in a genogroup I NLV outbreak were also tested. In sera from those infected with genogroup I NV or NLVs in volunteer and outbreak studies, only 3 of 25 were rMXV IgM positive; in contrast, 24 of 25 were IgM positive for recombinant NV (rNV). In sera from those infected with genogroup II NLVs in volunteer and outbreak studies, 28 of 47 were rMXV IgM positive and none were IgM positive for rNV, showing the specificity of each IgM test for its respective genogroup. In an outbreak of gastroenteritis not characterized as being of viral etiology but suspected to be due to NV, 7 of 13 persons had IgM responses to rMXV, whereas none had IgM responses to rNV, thus establishing the diagnosis as genogroup II NLV infection. The rMXV-based IgM capture ELISA developed is specific for the diagnosis of genogroup II NLV infections.

Brion, G., C. Viswanathan, et al. (2005). "Artificial neural network prediction of viruses in shellfish." Appl Environ Microbiol 71(9): 5244-53.
	A database was probed with artificial neural network (ANN) and multivariate logistic regression (MLR) models to investigate the efficacy of predicting PCR-identified human adenovirus (ADV), Norwalk-like virus (NLV), and enterovirus (EV) presence or absence in shellfish harvested from diverse countries in Europe (Spain, Sweden, Greece, and the United Kingdom). The relative importance of numerical and heuristic input variables to the ANN model for each country and for the combined data was analyzed with a newly defined relative strength effect, which illuminated the importance of bacteriophages as potential viral indicators. The results of this analysis showed that ANN models predicted all types of viral presence and absence in shellfish with better precision than MLR models for a multicountry database. For overall presence/absence classification accuracy, ANN modeling had a performance rate of 95.9%, 98.9%, and 95.7% versus 60.5%, 75.0%, and 64.6% for the MLR for ADV, NLV, and EV, respectively. The selectivity (prediction of viral negatives) was greater than the sensitivity (prediction of viral positives) for both models and with all virus types, with the ANN model performing with greater sensitivity than the MLR. ANN models were able to illuminate site-specific relationships between microbial indicators chosen as model inputs and human virus presence. A validation study on ADV demonstrated that the MLR and ANN models differed in sensitivity and selectivity, with the ANN model correctly identifying ADV presence with greater precision.

Brion, G. M., J. S. Meschke, et al. (2002). "F-specific RNA coliphages: occurrence, types, and survival in natural waters." Water Res 36(9): 2419-25.
	A small, well-defined watershed was investigated over a 2-year period to determine the prevalence of F-specific RNA coliphage (F + RNA) serotypes as indicators of animal fecal contamination. Sampling sites collected runoff from areas of urban and agricultural land use patterns. F-specific coliphages were concentrated from 2-L freshwater samples by polyethylene glycol precipitation, isolated using the double agar layer (DAL) method, confirmed as F + RNA by RNAse suppression, and serotyped. A subset of serotyped F + RNA were confirmed by genotyping. To determine relative survival, 10 confirmed F + RNA field isolates and 5 prototypic F + RNA were spiked into surface water and incubated at 25 degrees C for 36 days. F-specific coliphage isolation was strongly associated with rainfall events and was infrequent from primarily animal impacted surface waters. Field isolates were predoffiinantly Type I F + RNA (81%) and raw sewage isolates were predominantly Type III F + RNA (57%). Genotyping from either the watershed or raw sewage samples never positively identified Type IV F + RNA. Results from laboratory studies showed that F + RNA differ in their survival in water and that Type IV strains were the least persistent. Type III F + RNA were found to be reliably related to the release of uncontrolled human fecal material in the watershed, but the results of this study suggest that further study is required before utilizing for fecal source identification in natural waters.

Brockmann, R. A., D. D. Lenaway, et al. (1995). "Norwalk-like viral gastroenteritis: A large outbreak on a university campus." Journal of Environmental Health 57, no. 10: 19-22.
	A large outbreak of food-associated, nonbacterial gastroenteritis occurred on a university campus in November 1990. The case definition for illness over the three-day period fit 787 students for an overall attack rate of 13.1%. Several food workers were ill with similar symptoms 48 hours before the outbreak began, and two meals later consumed by students were found to be statistically associated with illness. The laboratory results, symptoms of illness, and the explosive spread of the disease are all consistent with other reports of Norwalk-like virus-mediated gastroenteritis in the literature. Although the descriptive epidemiology of the outbreak fit the typical Norwalk-like virus outbreak, electron microscopy studies did not definitively identify a viral particle as the causative agent. While more advanced techniques can often be useful, investigators should be aware of their shortcomings in actual practice, and may need to rely on traditional epidemiologic methods to determine the nature of a foodborne viral illness.

Brooks, H. A., R. M. Gersberg, et al. (2005). "Detection and quantification of hepatitis A virus in seawater via real-time RT-PCR." J Virol Methods 127(2): 109-18.
	A real-time RT-PCR method utilizing SYBR Green chemistry was developed to detect and enumerate hepatitis A virus (HAV) in ocean water. Ocean water samples were taken at the Tijuana River mouth (Tijuana, Mexico) and Imperial Beach pier (1.4 km north of the Tijuana River mouth in San Diego, California) following four separate rain events. A total of eight samples were collected, one from each location, each consisting of 4 l of ocean water. Using conventional RT-PCR and primers based on the conserved sequence at the VP3-VP1 genes of HAV, a 247 bp cDNA was amplified from six out of eight rain event water samples. HAV cDNA (confirmed by sequence analysis) was cloned into a TOPO vector (Invitrogen, Carlsbad, CA), and four primer sets were designed for application in SYBR Green real-time RT-PCR. The water samples were shown to contain inhibitors that affected real-time RT-PCR amplifications, however diluting the cDNA solution enabled successful amplification. Using real-time RT-PCR, HAV could be detected in all eight samples. Depending on the rain event, the viral load in these samples varied from 90 to 3523 copies of HAV/L of ocean water near the mouth of the Tijuana River, and 347 to 2656 copies/l near the Imperial Beach pier. The sensitivity, quantitative ability and the high throughput nature of SYBR Green real-time RT-PCR will be useful in monitoring HAV contamination in seawater.

Brown, B. A., D. R. Kilpatrick, et al. (2000). "Serotype-specific identification of enterovirus 71 by PCR." J Clin Virol 16(2): 107-12.
	BACKGROUND: Enterovirus 71 and coxsackievirus A16 are closely related genetically and are causative agents of hand foot and mouth disease. Because enterovirus 71 is more often associated with severe neurological disease, there is a need to rapidly discriminate between enterovirus 71 and coxsackievirus A16 during hand, foot, and mouth disease outbreaks. OBJECTIVES: Our goal was to develop and evaluate a serotype-specific reverse transcription-polymerase chain reaction (RT/PCR)-based typing method for enterovirus 71. STUDY DESIGN: Two sets of PCR primers were designed to match conserved amino acid intervals of enterovirus 71. One diagnostic primer pair contains deoxyinosine at sites of 4-fold codon degeneracy. A second primer pair was designed for use in sequencing and molecular epidemiology studies. Primer pairs were tested on strains encountered in routine diagnostic samples. RESULTS: Using both sets of primers on a panel of 61 prototype enteroviral strains, both primer pairs gave strong positive signals for only enterovirus 71. These primers amplified all enterovirus 71 isolates tested and discriminated between enterovirus 71 and the most closely related enterovirus, coxsackievirus A16. CONCLUSIONS: Our RT-PCR assay can be used for specific identification of enterovirus 71 clinical isolates. Furthermore, the 484-bp product of one primer pair has proven useful in sequencing studies to identify distinct genotypes of enterovirus 71.

Brown, C. M., J. W. Cann, et al. (2001). "Outbreak of Norwalk virus in a Caribbean island resort: application of molecular diagnostics to ascertain the vehicle of infection." Epidemiol Infect 126(3): 425-32.
	In 1998, an outbreak of gastroenteritis affected at least 448 persons including 122 staff at a resort hotel in Bermuda. A survey among staff indicated that gastroenteritis was associated with eating or drinking at the hotel (OR = 60, 95% CI = 2.4-15.1). Multiple specimens of drinking water had elevated faecal coliform levels and Escherichia coli present, suggestive of faecal contamination. Stools from 18 of the 19 persons with gastroenteritis that were tested were positive for genogroup-II Norwalk-like viruses (NLVs). RT-PCR analysis of a 31 specimen of water produced a genogroup-II NLV genome with a sequence identical to that of NLVs in the stools of three ill persons. This outbreak shows the value of new molecular diagnostics to link illness with a contaminated source through the use of sequence analysis. The risk of outbreaks such as these could be reduced in tourism dependent regions like Bermuda and the Caribbean by regular evaluation of data from the inspection and monitoring of drinking water supplies and waste water systems, by ensuring the chlorination of supplemental drinking water supplies and by establishing food-safety initiatives.

Brown, E. A., S. P. Day, et al. (1991). "The 5' nontranslated region of hepatitis A virus RNA: secondary structure and elements required for translation in vitro." Journal of Virology 65(11): 5828-5838.
	Although the lengthy 5' nontranslated regions (5'NTRs) of other picornaviral RNAs form highly ordered structures with important functions in viral translation, little is known about the 5'NTR of hepatitis A virus (HAV). We determined the nearly complete 5'NTR nucleotide sequences of two genetically divergent HAV strains (PA21 and CF53) and included these data in a comparative phylogenetic analysis of the HAV 5'NTR. We identified covariant nucleotide substitutions predictive of conserved secondary structures and used this information to develop a model of the 5'NTR secondary structure, which was further refined by thermodynamic predictions and nuclease digestion experiments. According to this model, the 5'NTR comprises six major structural domains. Domains I and II (bases 1 to 95) contain a 5'-terminal hairpin and two stem-loops followed by a single-stranded and highly variable pyrimidine-rich tract (bases 96 to 154). The remainder of the 5'NTR (domains III to VI, bases 155 to 734) contains several complex stem-loops, one of which may form a pseudoknot, and terminates in a highly conserved region containing an oligopyrimidine tract preceding the putative start codon by 13 bases. To determine which structural elements might function as an internal ribosome entry site, RNA transcripts representing the HAV 5'NTR with progressive 5' deletions were translated in rabbit reticulocyte lysates. The translation product was truncated, unprocessed P1 polyprotein. Removal of the 5'-terminal 354 bases of the 5'NTR had little effect on translation. However, deletion to base 447 slightly decreased translation, while deletion to base 533 almost completely abolished it. These data indicate that sequences 3' of base 355 play an important role in the translation mechanism utilized by genomic-length HAV RNA. Significantly, this region shares several conserved structural features with the internal ribosome entry site element of murine encephalomyocarditis virus. 

Brown, E. A., S. P. Day, et al. (1991). "Genetic variability within the 5' nontranslated region of hepatitis A virus RNA. Implications for secondary structure and function." Journal of Hepatology 13(4): S138-S143.
	The RNA genome of hepatitis A virus (HAV) contains a lengthy and relatively well conserved 5' nontranslated region (5'NTR). In other picornaviruses, the 5'NTR has been shown to have important functions related to the initiation of viral translation and replication of viral RNA, functions which are critically dependent on both primary and secondary RNA structure. We have utilized a phylogenetic approach to construct a model of the secondary structure of the HAV 5'NTR. By comparing the nucleotide sequences of genetically divergent simian and human HAV strains, we identified a series of covariant nucleotide substitutions which are predictive of conserved, double-stranded helical structures within the 5'NTR, and which thus permitted improved thermodynamic modeling of the secondary structure. The model was further refined based on the observed sites of cleavage of synthetic RNA by single- and double-strand specific RNAses. The results of these studies suggest that the 5'NTR of HAV has a general organization similar to that of other picornaviruses, and shares certain structural features and perhaps specific functions with the 5'NTRs of the cardioviruses and aphthoviruses. 

Brown, E. A., R. W. Jansen, et al. (1989). "Characterization of a simian hepatitis A virus (HAV): antigenic and genetic comparison with human HAV." Journal of Virology 63(11): 4932-4937.
	PA21, a strain of hepatitis A virus (HAV) recovered from a naturally infected captive owl monkey, is indistinguishable from human HAV in polyclonal radioimmunoassays and cross-neutralization studies. However, cDNA-RNA hybridization has suggested a significant difference at the genomic level between PA21 and a reference human virus, HM175. Further characterization of this unique HAV was undertaken in an effort to determine the extent of genetic divergence from human HAV and its relation to the conserved antigenic structure of the virus. The close similarity between PA21 and HM175 antigens was confirmed with an extended panel of 18 neutralizing murine monoclonal antibodies: a reproducible difference in binding to the two viruses was detected with only one antibody (B5-B3). The nucleotide sequence of the P1 region of the PA21 genome had only 83.2% identity with HM175 virus, a difference approximately twice as great as that found between any two human strains. Most nucleotide changes were in third base positions, and the amino acid sequences of the capsid proteins were largely conserved. Amino acid replacements were clustered in the carboxy terminus of VP1 and the amino-terminal regions of VP2 and VP1. These data indicate that PA21 virus represents a unique genotype of HAV and suggest the existence of an ecologically isolated niche for HAV among feral owl monkeys. 

Brown, G. C. (1949). "The possible significance of milk and water in the spread of virus infections." Am J Public Health 39(6): 764-771.
	
Brown, M., H. L. Wilson-Friesen, et al. (1992). "A block in release of progeny virus and a high particle-to-infectious unit ratio contribute to poor growth of enteric adenovirus types 40 and 41 in cell culture." J Virol 66(5): 3198-205.
	The fastidious enteric adenovirus (FEAd) types 40 (Ad40) and 41 (Ad41) are found in stool specimens of infants and young children in association with gastroenteritis. Although they can be isolated routinely from clinical specimens by using 293 cells, they are propagated with variable success in cell lines which support the replication of other adenovirus serotypes. HeLa cells are generally considered to be nonpermissive for the replication of FEAds, but in this study, Ad40 and Ad41 grew to comparable titers in individual 293 and HeLa cells. However, virus was not efficiently released from infected HeLa cells and thus did not undergo multiple cycles of infection in HeLa cell cultures. The block in virus release was not overcome in KB18 cells which, like 293 cells, constitutively express proteins encoded by the E1B region of a subgroup C adenovirus (in this case Ad2). Moreover, it was apparent from these studies that Ad40 and Ad41 have particle-to-infectious unit ratios several orders of magnitude greater than that for Ad5, even in 293 cells which express the E1A and E1B proteins of Ad5 and are considered to be permissive for replication of the FEAds. Neither the block in release of progeny virus nor the high particle-to-infectious unit ratio is explained solely by the defect in expression of the E1B 55K protein identified by Mautner et al. (V. Mautner, N. MacKay, and V. Steinthorsdottir, Virology 171:619-622, 1989; V. Mautner, N. MacKay, and K. Morris, Virology 179:129-138, 1990).

Brown, P. (2001). "Afterthoughts about bovine spongiform encephalopathy and variant Creutzfeldt-Jakob disease." Emerg Infect Dis 7(3 Suppl): 598-600.
	
Brown, P., L. Cervenakova, et al. (2001). "Blood infectivity and the prospects for a diagnostic screening test in Creutzfeldt-Jakob disease." J Lab Clin Med 137(1): 5-13.
	
Brown, P., R. G. Will, et al. (2001). "Bovine spongiform encephalopathy and variant Creutzfeldt-Jakob disease: background, evolution, and current concerns." Emerg Infect Dis 7(1): 6-16.
	The epidemic of bovine spongiform encephalopathy (BSE) in the United Kingdom, which began in 1986 and has affected nearly 200,000 cattle, is waning to a conclusion, but leaves in its wake an outbreak of human Creutzfeldt-Jakob disease, most probably resulting from the consumption of beef products contaminated by central nervous system tissue. Although averaging only 10-15 cases a year since its first appearance in 1994, its future magnitude and geographic distribution (in countries that have imported infected British cattle or cattle products, or have endogenous BSE) cannot yet be predicted. The possibility that large numbers of apparently healthy persons might be incubating the disease raises concerns about iatrogenic transmissions through instrumentation (surgery and medical diagnostic procedures) and blood and organ donations. Government agencies in many countries continue to implement new measures to minimize this risk.

Brown, T. S., J. F. M. Jr., et al. (1974). "Virus removal by diatomaceous-earth filtration-Part 1." Journal of the American Water Works Association: 98-102.
	This study, involving the removal of bacterial virus from water using diatomaceous-earth filter aids, covers the comparative properties of uncoated and polyelectrolye-coated products as they affect the process. The work is based on studies using bacteriophage T2 for Escherichia coli. 

Brown, V. K. and B. H. Robertson (1990). "Immunoselection of clinical specimens containing virus followed by polymerase chain reactor amplification and rapid direct sequencing." BioTechniques 8(3): 262-264.
	no abstract

Bruce, M. E., A. Boyle, et al. (2002). "Strain characterization of natural sheep scrapie and comparison with BSE." J Gen Virol 83(Pt 3): 695-704.
	Scrapie was transmitted to mice from ten sheep, collected in the UK between 1985 and 1994. As in previous natural scrapie transmissions, the results varied between scrapie sources in terms of the incidence of disease, incubation periods and neuropathology in challenged mice. This contrasted with the uniformity seen in transmissions of BSE to mice. The scrapie and BSE isolates were characterized further by serial passage in mice. Different TSE strains were isolated from each source according to the Sinc or PrP genotype of the mouse used for passage. The same two mouse-passaged strains, 301C and 301V, were isolated from each of three BSE sources. Despite the variation seen in the primary transmissions of scrapie, relatively few mouse-passaged scrapie strains were isolated and these were distinct from the BSE-derived strains. The ME7 scrapie strain, which has often been isolated from independent sheep sources in the past, was identified in isolates from four of the sheep. However, a new distinct strain, 221C, was derived from a further four scrapie sheep. These results suggest that there is agent strain variation in natural scrapie in sheep and that the spectrum of strains present may have changed over the last 20 years. The tested sample is too small to come to any conclusions about whether the BSE strain is present in sheep, but the study provides a framework for further more extensive studies.

Brugh Jr., M. (1977). "Butylated hydroxytoluene protects chickens exposed to Newcastle disease virus." Science 197(4310): 1291-1292.
	Dietary butylated hydroxytoluene, an antioxidant widely used in food and feed processing, prevents mortality of chickens exposed to virulent Newcastle disease virus and prevents the serological response of chickens exposed to avirulent Newcastle disease virus. This chemoprophylactic effect is evident when chickens are fed diets containing concentrations of butylated hydroxytoluene normally used for antioxidant purposes (100 to 200 parts per million of total diet). 

Brugha, R., I. Vipond, et al. (1999). " A community outbreak of food-borne small round-structured virus gastroenteritis caused by a contaminated water supply." Epidemiology and Infection 122(1): 145-54.
	In August 1994, 30 of 135 (23%) bakery plant employees and over 100 people from South Wales and Bristol in the United Kingdom, were affected by an outbreak of gastroenteritis. Epidemiological studies of employees and three community clusters found illness in employees to be associated with drinking cold water at the bakery (relative risk 3.3, 95%, CI 1.6-7.0), and in community cases with eating custard slices (relative risk 19.8, 95%, CI 2.9-135.1) from a variety of stores supplied by one particular bakery. Small round-structured viruses (SRSV) were identified in stool specimens from 4 employees and 7 community cases. Analysis of the polymerase and capsid regions of the SRSV genome by reverse transcription-polymerase chain reaction (RT-PCR) demonstrated viruses of both genogroups (1 and 2) each with several different nucleotide sequences. The heterogeneity of the viruses identified in the outbreak suggests that dried custard mix may have been inadvertently reconstituted with contaminated water. The incident shows how secondary food contamination can cause wide-scale community gastroenteritis outbreaks, and demonstrates the ability of molecular techniques to support classical epidemiological methods in outbreak investigations.

Bruguera, M., J. M. Bayas, et al. (1996). "Immunogenicity and reactogenicity of a combined hepatitis A and B vaccine in young adults." Vaccine 14(15): 1407-1411.
	The aim of this study was to assess the immunogenicity and reactogenicity of a combined vaccine against hepatitis A virus (HAV) and hepatitis B virus (HBV) in young healthy adults. A total of 150 subjects (20 +/- 1.4 years; 111 females and 39 males) negative for anti-HAV, anti-HBs, anti-HBc and HBsAg markers, were enrolled and randomized to received the study vaccine from one of the three lots under double blind conditions. Three doses of the combined vaccine were administered by intramuscular route (deltoid) following a 0-, 1- and 6 months schedule. Each dose of 1 ml contained at least 720 ELISA Units of HAV antigen (Strain HM175) and 20 micrograms of recombinant HBsAg. Blood samples for anti-HAV (ELISA), anti-HBs (RIA) and transaminases determinations were obtained 1 month after the administration of each dose and before to the administration of the third dose (month 6). Local and general reactions were recorded by the vaccinee on the day of each vaccination and for the three following days on symptom sheets. A total of 147 subjects completed the study. There were not statistically significant differences between groups regarding to immunogenicity. All subjects had seroconverted [geometric mean titres (GMT): 1311 mIU ml-1] for hepatitis A component following the second dose; GMT increased to 8895 mIU ml-1 after the third dose. Seroconversion rates for hepatitis B component were 98% (GMT, 104 mIU ml-1) after the second dose and 100% after the third dose (GMT, 7097 mIU ml-1). There were not statistically significant differences between groups regarding to incidence of local and general symptoms. Soreness at the injection site and headache were the most commonly local and general symptoms reported, following 42% and 11% of the doses, respectively. This vaccine when given to young adults was well tolerated and induced high immunogenic response, similar to that obtained by hepatitis A and hepatitis B vaccines administered separately in previously reported trials. 

Bryan, J. P., S. A. Tsarev, et al. (1994). "Epidemic hepatitis E in Pakistan: patterns of serologic response and evidence that antibody to hepatitis E virus protects against disease." J Infect Dis 170(3): 517-21.
	IgM and IgG anti-hepatitis E virus (HEV) patterns were determined in sera collected during a hepatitis outbreak in Pakistan. HEV infection was detected serologically in 122 patients. IgM anti-HEV was detected in specimens collected up to 2 weeks before and 5-7 weeks after hospitalization in 91% and 100%, respectively, of 122 HEV-infected patients. IgG followed a similar pattern. Peak antibody titers appeared 2-4 weeks after hospitalization. At 20 months after hospitalization, IgM anti-HEV was not detected in any of 33 patients; IgG was found in all. IgG anti-HEV appeared to be protective in contracts of patients. This study confirms HEV as the cause of the outbreak, quantifies IgM and IgG anti-HEV responses, provides evidence that IgG anti-HEV protects against hepatitis E, and demonstrates that IgG anti-HEV persists, but at diminished titer, after infection. Hepatitis E in young adults is the result of primary infection with HEV and, if reinfection occurs, it does not commonly cause serious illness.

Brydone, T. J., J. Adams, et al. (1990). "Beaters on the run -the pheasant's revenge?" Communicable Disease Weekly Report, Scotland 90(43): 6-9.
	
Buck, C. E., M. A. Emerson, et al. (1982). "Ozone Inactivation of Cell-Associated Viruses." Applied and Environmental Microbiology 43, no. 3: 603-608.
	The inactivation of HEp-2 cell-associated poliovirus (Sabin 1) and coxsackie-virus A9 was investigated in three experimental systems, usign ozone as a disinfectant. The cell-associated poliovirus and coxsackievirus samples demonstrated survival in a continuous-flow ozonation system at applied ozone dosages of 4.06 and 4.68 mg/liter, respectively, for 30 s. Unassociated viral controls were inactivated by the application of 0.081 mg of ozone per liter for 10 s. The batch reactor with a declining ozone residual did not effect total inactivation of either cell-associated enteric virus. These cell-associated viruses were completely inactivated after exposure to ozone in a batch reactor using continuous ozonation. Inactivation of cell-associated poliovirus required a 2-min contact period with an applied ozone dosage of 6.82 mg/liter and a residual ozone concentration of 4.70 mg/liter, whereas the coxsackievirus was completely inactivated after a 5-min exposure to an applied ozone dosage of 4.81 mg/liter with an ozone residual of 2.18 mg/liter. These data indicate that viruses associated with cells or cell fragments are protected from inactivation by ozone concentrations that readily inactivate purified virus.

Buckow, R., S. Isbarn, et al. (2008). "Predictive model for inactivation of feline calicivirus, a norovirus surrogate, by heat and high hydrostatic pressure." Appl Environ Microbiol 74(4): 1030-8.
	Noroviruses, which are members of the Caliciviridae family, represent the leading cause of nonbacterial gastroenteritis in developed countries; such norovirus infections result in high economic costs for health protection. Person-to-person contact, contaminated water, and foods, especially raw shellfish, vegetables, and fruits, can transmit noroviruses. We inactivated feline calicivirus, a surrogate for the nonculturable norovirus, in cell culture medium and mineral water by heat and high hydrostatic pressure. Incubation at ambient pressure and 75 degrees C for 2 min as well as treatment at 450 MPa and 15 degrees C for 1 min inactivated more than 7 log10 PFU of calicivirus per ml in cell culture medium or mineral water. The heat and pressure time-inactivation curves obtained with the calicivirus showed tailing in the logarithmic scale. Modeling by nth-order kinetics of the virus inactivation was successful in predicting the inactivation of the infective virus particles. The developed model enables the prediction of the calicivirus reduction in response to pressures up to 500 MPa, temperatures ranging from 5 to 75 degrees C, and various treatment times. We suggest high pressure for processing of foods to reduce the health threat posed by noroviruses.

Buesa, J., B. Collado, et al. (2002). "Molecular epidemiology of caliciviruses causing outbreaks and sporadic cases of acute gastroenteritis in Spain." J Clin Microbiol 40(8): 2854-9.
	The molecular epidemiology of human caliciviruses (HuCVs) causing sporadic cases and outbreaks of acute gastroenteritis around eastern Spain (Catalonia and the Valencian Community) was studied by reverse transcription-PCR (RT-PCR) and by sequencing part of the RNA polymerase gene in open reading frame 1. HuCVs were detected in 44 of 310 stool specimens (14.19%) negative for other enteric pathogens obtained from children with acute gastroenteritis. Norwalk-like viruses (NLVs) were the most common cause of the gastroenteritis outbreaks investigated here. They were detected in 14 out of 25 (56%) outbreaks with an identified pathogen. Genotypes producing both sporadic cases and outbreaks were diverse, with a predominance of GGII strains related to genotypes Melksham and Lordsdale. Five strains clustered with a "new variant" designated GGIIb, which was detected circulating throughout quite a few European countries in the years 2000 and 2001. The emergence mechanism of these strains might be the occurrence of intertypic recombinations between different viruses. The nucleotide sequence of part of the capsid gene (ORF2) from three of these strains demonstrated their relationship with Mexico virus.

Buisson, Y., P. Coursaget, et al. (1994). "Hepatitis E virus infection in soldiers sent to endemic regions." Lancet 344(8930): 1165-1166.
	
Bull, I. D., M. J. Lockheart, et al. (2002). "The origin of faeces by means of biomarker detection." Environ Int 27(8): 647-54.
	
Bull, R. A., E. T. Tu, et al. (2006). "Emergence of a new norovirus genotype II.4 variant associated with global outbreaks of gastroenteritis." J Clin Microbiol 44(2): 327-33.
	Norovirus (NoV) is highly infectious and is the major cause of outbreak gastroenteritis in adults, with pandemic spread of the virus being reported in 1995 and 2002. The NoV genome is genetically diverse, which has hampered development of sensitive molecular biology-based methods. In this study we report on a nested reverse transcriptase PCR (nRT-PCR) that was designed to amplify the highly conserved 3' end of the polymerase region and the 5' end of the capsid gene of NoV genogroup II (GII). The nRT-PCR was validated with strains isolated from sporadic and outbreak cases between 1997 and 2004 in New South Wales, Australia. Phylogenetic analysis identified six genotypes circulating in New South Wales, GII.1, GII.3, GII.4, GII.6, GII.7, and GII.10, with GII.4 being the predominant genotype. In 2004, there was a marked increase in NoV GII activity in Australia, with a novel GII.4 variant being identified as the etiological agent in 18 outbreaks investigated. This novel GII.4 variant, termed Hunter virus, differed by more than 5% at the amino acid level across the capsid from any other NoV strain in the GenBank and EMBL databases. The Hunter virus was subsequently identified as the etiological agent in large epidemics of gastroenteritis in The Netherlands, Japan, and Taiwan in 2004 and 2005.

Burge, W. D., W. N. Cramer, et al. (1983). "Effect of heat on virus inactivation by ammonia." Appl Environ Microbiol 46(2): 446-51.
	The rate of inactivation of bacteriophage f2 and poliovirus 1 (CHAT) by NH3 was strongly influenced by temperature. The process was pseudo-first order at all temperatures and NH3 concentrations. Poliovirus was inactivated at a greater rate than f2, but the change in the rate of inactivation with increasing temperature in the range of approximately 10 to 40 degrees C was greater for f2 than for poliovirus. At higher temperatures, the rate of change was greater for poliovirus. Arrhenius plots of the data were biphasic, indicating that two inactivation processes were occurring, one for the low temperature range and another for the high temperature range. However, the magnitudes of the thermodynamic variables for f2 were low enough, as calculated for the low (10 to 35 degrees C) and high (35 to 60 degrees C) phases, that inactivation could have occurred by breakage of nucleic acid chains. For poliovirus, the sizes indicated possible involvement of nucleic acid at the low temperatures (10 to 40 degrees C) but some unknown mechanism for the high temperatures (40 and 50 degrees C).

Burkhardt III, W., W. D. Watkins, et al. (1992). "Seasonal effects on accumulation of microbiol indicator organisms by Mercenaria mercenaria." Applied and Environmental Microbiology 58(3): 826-831.
	The ability of hard-shelled clams (Mercenaria mercenaria) to accumulate fecal coliforms and other microorganisms (Escherichia coli, Clostridium perfringens, and male-specific bacteriophages) was determined over a 1-year period. Twenty separate trails were conducted during different seasons to encompass a wide range of water temperatures. The greatest accumulation of microorganisms in hard-shelled clams occurred during certain periods in the spring, at temperatures ranging from 11.5 to 21.5 degrees C. These periods of hyperaccumulation did not always coincide for all organisms; the accumulation of bacteriophages was not predicted by the accumulation of either fecal coliforms or C. perfringens. Bacteriophages and C. perfringens showed significantly higher rates of accumulation than either the fecal coliform group or E. coli, especially during the spring. The higher incidence of human viral gastroenteritis associated with the consumption of shellfish during this period may be a result of the extraordinary concentration of certain microorganisms, including enteric viral pathogens. 

Burkhardt, W. r. C. K. (2000). "Selective accumulation may account for shellfish-associated viral illness." Applied and Environmental Microbiology 66(4): 1375-8.
	From 1991 through 1998, 1,266 cases of shellfish-related illnesses were attributed to Norwalk-like viruses. Seventy-eight percent of these illnesses occurred following consumption of oysters harvested from the Gulf Coast during the months of November through January. This study investigated the ability of eastern oysters (Crassostrea virginica) to accumulate indicator microorganisms (i.e., fecal coliforms, Escherichia coli, Clostridium perfringens, and F(+) coliphage) from estuarine water. One-week trials over a 1-year period were used to determine if these indicator organisms could provide insight into the seasonal occurrence of these gastrointestinal illnesses. The results demonstrate that oysters preferentially accumulated F(+) coliphage, an enteric viral surrogate, to their greatest levels from late November through January, with a concentration factor of up to 99-fold.  However, similar increases in accumulation of the other indicator microorganisms were not observed. These findings suggest that the seasonal occurrence of shellfish-related illnesses by enteric viruses is, in part, the result of seasonal physiological changes undergone by the oysters that affect their ability to accumulate viral particles from estuarine waters.

Burns, K. F., D. F. Shelton, et al. (1958). "Bat rabies: experimental host transmission studies." Annals of New York Academy of Science 70: 452-466.
	not available

Burton-MacLeod, J. A., E. M. Kane, et al. (2004). "Evaluation and comparison of two commercial enzyme-linked immunosorbent assay kits for detection of antigenically diverse human noroviruses in stool samples." J Clin Microbiol 42(6): 2587-95.
	Two recently commercialized enzyme-linked immunosorbent assay kits, the SRSV(II)-AD (Denka Seiken Co. Ltd., Tokyo, Japan) and IDEIA NLV (DakoCytomation Ltd., Ely, United Kingdom) kits, that detect human norovirus (HuNV) antigens in stool samples were evaluated to assess whether they could be used instead of reverse transcription-PCR (RT-PCR) for routine diagnosis. The sensitivities and specificities of the two kits were tested with a panel of 103 stool samples containing HuNVs of 4 and 10 genetic subgroups within genogroups I and II (GI and GII), respectively, and 39 stool samples containing other enteric viruses. The Denka kit had a high sensitivity (>70% for 10 of the 14 subgroups) but a specificity of only 69%, and the Dako kit had a low sensitivity (<30% for 6 GII subgroups) but a high specificity of 100%. Statistical analysis suggests that HuNVs of four subgroups (subgroups GII/2, GII/5, GII/6, and GII/n) are likely to elude detection by the Dako kit. The two kits also demonstrated differences in reactivities. While the Dako kit discriminated between the GI and GII antigens of HuNVs, the Denka kit cross-reacted with samples containing all GI and GII subgroups of HuNVs. Moreover, the Denka kit also reacted with samples containing human sapovirus (HuSV). We demonstrate that the cross-reactivity of the Denka kit is not due to specific reactions with HuNV and HuSV antigens. These results indicate that neither the Denka kit nor the Dako kit has all the performance characteristics required to replace the RT-PCR methods used to detect HuNVs.

Butchaiah, G. (1988). "Infectivity assay of bovine rotavirus: evaluation of plaque and end-point methods in comparison with immunofluorescent cell assay." Acta Virol 32(1): 60-4.
	Three different methods, namely plaque assay, immunofluorescent cell (IFC) count and end-point dilution (TCID50) were evaluated for quantitative infectivity assay of the cell culture adapted UK strain of bovine rotavirus in secondary calf kidney (CK) cells and BGM cell line. Plaque and IFC count techniques were found equally efficient for infectivity titration of bovine rotavirus. Addition of trypsin into maintenance medium enhanced the sensitivity of the TCID50 method. Both CK and BGM cells served as efficient assay cells for infectivity assay of bovine rotavirus by IFC count and TCID50 methods, whereas, for plaque assay, only CK cells were found suitable.

Buti, M., P. Clemente-Casares, et al. (2004). "Sporadic cases of acute autochthonous hepatitis E in Spain." J Hepatol 41(1): 126-31.
	BACKGROUND/AIMS: In industrialized countries hepatitis E virus (HEV) infection is rare and its diagnosis is difficult because the utility of available tests is not well established. METHODS: We studied the presence of acute HEV infection markers in a cluster of 11 cases of acute hepatitis with IgG anti-HEV antibodies. RESULTS: Three cases were confirmed as acute hepatitis E and 8 as presumptive hepatitis E, two as a past HEV infection and one could not be determined. Three different HEV strains were identified in serum from 3 patients. Two strains belonged to genotype 3, the predominant genotype found in local urban sewage and the other strain belonged to genotype 1 and was considered an imported strain. CONCLUSIONS: Our findings demonstrate the presence of some autochthonous, sporadic acute hepatitis E cases as well as an imported case in our area and the transitory nature of virological and serological markers for HEV.

Butot, S., T. Putallaz, et al. (2007). "Attachment of enteric viruses to bottles." Appl Environ Microbiol 73(16): 5104-10.
	Storage of water that was deliberately contaminated with enteric viruses in polyethylene terephthalate (PET) bottles led to a rapid decrease of the apparent viral load, thereby hampering the development of samples for a collaborative evaluation of viral detection methods for bottled water. To determine if this decrease was due to spontaneous inactivation or to adhesion, an elution protocol was developed and combined with a rapid and sensitive real-time reverse transcription-PCR-based method to quantify adsorbed norovirus (NV), hepatitis A virus (HAV), and rotavirus (RV) on bottle walls. The NV retention on PET bottle walls after 20 and 62 days reached an average level of 85% and 95% of the recovered inoculum, respectively. HAV and RV also showed adsorption onto PET bottles, reaching 90% and 80%, respectively, after 20 days of storage. NV and RV attachment was demonstrated to be dependent on the presence of autochthonous flora, whereas HAV adsorption was independent of it. Application of the elution and viral detection protocol to 294 commercially available water bottles obtained from 25 different countries did not give any positive result, thereby providing further evidence that the sources used for this product are free from enteric viruses and support for the theory that bottled water is not a vehicle for viral diseases.

Butot, S., T. Putallaz, et al. (2007). "Procedure for rapid concentration and detection of enteric viruses from berries and vegetables." Appl. Environ. Microbiol. 73(1): 186-192.
	Several hepatitis A virus (HAV) and norovirus (NV) outbreaks due to consumption of berries and vegetables have been reported during recent years. To facilitate the detection of enteric viruses that may be present on different fresh and frozen products, we developed a rapid and sensitive detection method for HAV, NV, and rotavirus (RV). Initial experiments focused on optimizing the composition of the elution buffer, improving the viral concentration method, and evaluating the performance of various extraction kits. Viruses were extracted from the food surface by a direct elution method in a glycine-Tris (pH 9.5) buffer containing 1% beef extract and concentrated by ultrafiltration. Occasionally, PCR inhibitors were present in the processed berry samples, which gave relatively poor detection limits. However, this problem was overcome by adding a pectinase treatment in the protocol, which markedly improved the sensitivity of the method. After optimization, this concentration method was applied in combination with real-time reverse transcription-PCR (RT-PCR) using specific primers in various types of berries and vegetables. The average detection limits were 1 50% tissue culture infective dose (TCID(50)), 54 RT-PCR units, and 0.02 TCID(50) per 15 g of food for HAV, NV, and RV, respectively. Based on our results, it is concluded that this procedure is suitable to detect and quantify enteric viruses within 6 h and can be applied for surveillance of enteric viruses in fresh and frozen products.

Butot, S., T. Putallaz, et al. (2008). "Effects of sanitation, freezing and frozen storage on enteric viruses in berries and herbs." Int. J. Food Microbiol. 126(1-2): 30-35.
	Norovirus (NV) and hepatitis A virus (HAV) are foodborne enteric viruses associated with outbreaks of disease following consumption of fresh or frozen produce. Model experiments were performed to determine the effectiveness of certain commercial processes for the removal of enteric viruses that might be present in berries and herbs. The survival and persistence of HAV, NV, rotavirus (RV) and feline calicivirus (FCV), a surrogate for NV, in frozen produce over time were determined. Survival and inactivation of HAV, RV and FCV were assessed by viral culture and quantitative reverse transcription-PCR (RT-PCR), whereas NV persistence was determined by quantitative RT-PCR only. Freezing did not significantly reduce the viability of any of the viruses except the infectivity of FCV in strawberries. Frozen storage for 3 months had limited effects on HAV and RV survival in all tested food products, whereas in frozen raspberries and strawberries FCV infectivity showed the highest decay rate due to acid pH. To simulate postharvesting conditions, fresh berries and herbs were rinsed with tap, warm or chlorinated water or with a chlorine dioxide (ClO(2)) solution. Available chlorine at a concentration of 200 ppm and ClO(2) at 10 ppm reduced measurable enteric viruses in raspberry and parsley samples by less than 2 log(10) units.

Butt, A. A., K. E. Aldridge, et al. (2004). "Infections related to the ingestion of seafood Part I: Viral and bacterial infections." Lancet Infect Dis 4(4): 201-12.
	Foodborne diseases cause an estimated 76 million illnesses in the USA each year. Seafood is implicated in 10-19% of these illnesses. A causative agent can be traced in about 44% of seafood-related outbreaks, viruses accounting for around half of these illnesses. Although viruses are the most common cause of seafood-related infections, most hospitalisations and deaths are due to bacterial agents. A wide variety of viruses, bacteria, and parasites have been implicated in seafood-related outbreaks, which are reported worldwide. The factor most commonly associated with infection is consumption of raw or undercooked seafood. People with underlying disorders, particularly liver disease, are more susceptible to infection. The first part of this two-part review summarises the general incidence of seafood-related infections and discusses the common viral and bacterial causes of these infections. For each agent, the microbiology, epidemiology, mode of transmission, and treatment are discussed. In the May issue of the journal we will discuss parasites associated with seafood consumption, the safety of seafood, and the measures put in place in the USA to increase its safety.

Butz, A. M., P. Fosarelli, et al. (1993). "Prevalence of rotavirus on high-risk fomites in day-care facilities." Pediatrics 92(2): 202-5.
	STUDY OBJECTIVE. The objective of this study was to determine the prevalence of rotavirus contamination on environmental surfaces in day-care environments, using the polymerase chain reaction technique. DESIGN. High-risk fomites were identified in two day-care centers and sampled biweekly during a 6-month study period. Water samples from water-play tables in each center were also collected during the study period. During an infectious disease outbreak, fomites were sampled from the rooms in which the outbreak occurred. Reverse transcriptase/polymerase chain reaction was carried out for viral detection of rotavirus from the fomites, and standard bacteriologic measures were used to detect bacteria in samples from water-play tables. RESULTS. A total of 96 fomite samples were tested for presence of rotavirus from the two centers, of which 18/96 (19%) tested positive for rotavirus. The timing of the positive samples differed between the two centers. In the center that housed infants, a peak of rotavirus-positive fomites coincided with two enteric outbreaks. Rotavirus contamination was found on the telephone receiver, drinking fountain, water-play table, and toilet handles in both centers. Bacteria in large quantities were also identified in water-play table samples. CONCLUSIONS. Moist surfaces including the telephone, water fountains, and water-play tables are common sources of rotavirus contamination within the day-care environment. Until a safe and affordable drug or vaccine against rotavirus is available for general use, avoidance of rotaviral infections is the most effective method for the prevention of rotavirus gastroenteritis.

Caballero, S., S. Guix, et al. (2003). "Persistent gastroenteritis in children infected with astrovirus: association with serotype-3 strains." J Med Virol 71(2): 245-50.
	The relationship between cases of persistent diarrhoea and the levels and type of human astrovirus was investigated. The potential correlation between human astrovirus excretion levels and the occurrence of protracted gastroenteritis was elucidated after quantifying astroviruses in faecal samples by a competitive RT-PCR. This assay was developed employing an internal RNA standard constructed for this purpose and showed a threshold of positivity of 3.4 x 10(4) genomes per gram of faeces. By this procedure, the levels of astrovirus, belonging to serotypes 1, 2, 3, 4, and 8, in faecal samples could be ascertained to range from 3.4 x 10(8) to 1 x 10(13) per gram of faeces. The mean viral titre in the serotype 3-containing faeces was higher than in any of the other serotype-containing samples. In children with no background disease, persistent gastroenteritis cases were detected in 8.5% of the astrovirus infections, and 37.5% of those were associated with astrovirus type 3 infection. In addition, 42.9% of astrovirus 3 isolates were implicated with persistent cases, some of them lasting for 3 months. Other type 3 isolates, detected in the faeces in very large numbers, caused severe gastroenteritis.

Caceres, V. M., D. K. Kim, et al. (1998). "A viral gastroenteritis outbreak associated with person-to-person spread among hospital staff." Infect Control Hosp Epidemiol 19(3): 162-7.
	OBJECTIVE: To identify the etiologic agent and risk factors associated with a hospital ward outbreak of gastroenteritis. SETTING: A regional referral hospital in upstate South Carolina. METHODS: We reviewed patient charts, surveyed staff, and tested stool from acutely ill persons. A case was defined as diarrhea and vomiting in a staff member or patient from January 5 to 13, 1996. RESULTS: The initial case occurred on January 5 in a staff nurse who subsequently was hospitalized on the ward and visited by many staff colleagues. The staff were at a significantly greater risk for gastroenteritis than were patients (28/89 [31%] vs 10/91 [11%]; relative risk [RR], 2.9; 95% confidence interval [CI95], 1.5-5.5). All 10 case-patients had been exposed to case-nurses (assigned nurses who were primary caretakers), and eight had documented exposure to case-nurses 1 to 2 days before their illness. Patients exposed to case-nurses had a significantly increased risk of illness (8/57 [14%] vs 0/32; RR, >4.5; CI95, undefined). Neither staff nor patients had significantly increased risk from food, water, ice, or exposure to case-patients. Electron microscopy identified small round-structured viruses (SRSVs) in nine of nine stool samples. CONCLUSION: This nosocomial outbreak of gastroenteritis was likely caused by SRSVs introduced by a staff member and spread via person-to-person transmission from and among staff. The potential for spread of SRSV-associated gastroenteritis from and among staff should be considered in developing strategies to prevent similar outbreaks in hospital settings.

Cacopardo, B., R. Russo, et al. (1997). "Acute hepatitis E in Catania (eastern Sicily) 1980-1994. The role of hepatitis E virus." Infection 25(5): 313-6.
	Between 1980 and 1994, 540 patients with acute viral hepatitis were admitted to hospital at the Department of Infectious Diseases of Catania (eastern Sicily). Twenty-five patients out of 540 were assessed as having non-A, non-B, non-C hepatitis. These subjects were studied for anti-HEV IgM and IgG seroprevalence by testing serial serum samples collected 1, 4, 12 and 24 weeks after the onset of acute disease. Fourteen of 25 samples (56%) seroconverted to anti-HEV IgG antibodies. No sample was positive for anti-HEV IgG at week 1, ten samples were positive at week 4 and the remainder at week 12. Anti-HEV reactivity was maintained until week 24 in all cases. In 11 of the 14 patients seroconverting to anti-HEV, the presence of IgM anti-HEV was found, which appeared in the sample from week 1 and gradually disappeared thereafter. Identified risk factors for HEV transmission included travel in the tropics and shellfish ingestion (anti-HEV positive versus anti-HEV negative: p < 0.05). HEV-related hepatitis is not yet a major public health problem in Sicily but, from our data, the trend of its incidence is clearly upwards. The high incidence of faecally-orally transmitted diseases in Sicily, the crucial position of Sicily in the middle of the Mediterranean Sea (where HEV largely circulates) and the increase of migration from developing countries are all factors which should increase awareness for a more active surveillance of the spread of HEV in our area.

Calci, K. R., W. Burkhardt, 3rd, et al. (1998). "Occurrence of male-specific bacteriophage in feral and domestic animal wastes, human feces, and human-associated wastewaters." Appl Environ Microbiol 64(12): 5027-9.
	Male-specific bacteriophage (MSB) densities were determined in animal and human fecal wastes to assess their potential impact on aquatic environments. Fecal samples (1,031) from cattle, chickens, dairy cows, dogs, ducks, geese, goats, hogs, horses, seagulls, sheep, and humans as well as 64 sewerage samples were examined for MSB. All animal species were found to harbor MSB, although the great majority excreted these viruses at very low levels. The results from this study demonstrate that in areas affected by both human and animal wastes, wastewater treatment plants are the principal contributors of MSB to fresh, estuarine, and marine waters.

Calci, K. R., G. K. Meade, et al. (2005). "High-pressure inactivation of hepatitis A virus within oysters." Appl. Environ. Microbiol. 71(1): 339-343.
	Previous results demonstrated that hepatitis A virus (HAV) could be inactivated by high hydrostatic pressure (HHP) (D. H. Kingsley, D. Hoover, E. Papafragkou, and G. P. Richards, J. Food Prot. 65:1605-1609, 2002); however, direct evaluation of HAV inactivation within contaminated oysters was not performed. In this study, we report confirmation that HAV within contaminated shellfish is inactivated by HHP. Shellfish were initially contaminated with HAV by using a flowthrough system. PFU reductions of >1, >2, and >3 log(10) were observed for 1-min treatments at 350, 375, and 400 megapascals, respectively, within a temperature range of 8.7 to 10.3 degrees C. Bioconcentration of nearly 6 log(10) PFU of HAV per oyster was achieved under simulated natural conditions. These results suggest that HHP treatment of raw shellfish will be a viable strategy for the reduction of infectious HAV.

Calder, L., G. Simmons, et al. (2003). "An outbreak of hepatitis A associated with consumption of raw blueberries." Epidemiol Infect 131(1): 745-51.
	This report describes the epidemiology, investigation and control of a hepatitis A (HAV) outbreak in New Zealand. Descriptive and analytical epidemiology, virology, product traceback and an orchard investigation were carried out. A case-control study revealed that 56% of 39 cases had consumed raw blueberries, compared with 14% of 71 controls (odds ratio 7.6; 95% confidence intervals 2.6-22.4). Traceback of product through retailers and wholesalers implicated a single commercial orchard. Hepatitis A virus was detected by reverse transcriptase polymerase chain reaction in faecal specimens from cases as well as a blueberry product from the orchard. Presence of hepatitis A virus was confirmed by DNA hybridization and sequencing of PCR products. Sanitary audit of the orchard revealed multiple opportunities for contamination of blueberries by pickers. This outbreak highlights the need for food safety programmes in the berry fruit industry.

Calderon, R. L. and G. F. Craun (2006). "Estimates of endemic waterborne risks from community-intervention studies." J Water Health 4 Suppl 2: 89-99.
	The nature and magnitude of endemic waterborne disease are not well characterized in the United States. Epidemiologic studies of various designs can provide an estimate of the waterborne attributable risk along with other types of information. Community drinking water systems frequently improve their operations and may change drinking water treatment and their major source of water. In the United States, many of these treatment changes are the result of regulations promulgated under the Safe Drinking Water Act. A community-intervention study design takes advantage of these "natural" experiments to assess changes in health risks. In this paper, we review the community-intervention studies that have assessed changes in waterborne gastroenteritis risks among immunocompetent populations in industrialized countries. Published results are available from two studies in Australia, one study in the United Kingdom, and one study in the United States. Preliminary results from two other US studies are also available. Although the current information is limited, the risks reported in these community-intervention studies can help inform the national estimate of endemic waterborne gastroenteritis. Information is provided about endemic waterborne risks for unfiltered surface water sources and a groundwater under the influence of surface water. Community-intervention studies with recommended study modifications should be conducted to better estimate the benefits associated with improved drinking water treatment.

Calderon-Margalit, R., R. Sheffer, et al. (2005). "A large-scale gastroenteritis outbreak associated with Norovirus in nursing homes." Epidemiol Infect 133(1): 35-40.
	An increase in gastroenteritis outbreaks due to Norovirus has been reported worldwide. We investigated a large-scale outbreak affecting 246 residents and 33 staff members in six nursing homes in the Tel-Aviv district, Israel, during 3 weeks in 2002. Person-to-person spread was noticed in all nursing homes. The spread of disease could not be attributed to social interactions. Among the elderly residents, the hospitalization rate was 10.2% and the case-fatality rate was 2.0%. Bacteriological cultures were negative. Overall, 7 out of 15 stool specimens were positive for Norovirus by RT-PCR. All were sequenced and found to be 90% identical. The characteristics of this outbreak and the RT-PCR results suggest that illness was caused by Norovirus. Due to the high case-fatality rate of Norovirus gastroenteritis, there should be a high index of suspicion when encountering a gastroenteritis outbreak among the elderly. This will enable prompt action to stop the spread of illness.

Callahan, K. M., D. J. Taylor, et al. (1995). "Comparative survival of hepatitis A virus, poliovirus and indicator viruses in geographically diverse seawaters." Water Science and Technology 31(5-6): 189-193.
	
Callis, J. J., J. L. Hyde, et al. (1975). "Survival of foot-and-mouth disease virus in milk and milk products." Bulletin du Office International des Epizooties 83: 181-191.
	not available

Campbell (1943). "An outbreak of jaundice." Health Bull. (Edinburgh) 2: 64.
	
Canada, H. a. W. (1980). "Foodborne and waterborne disease in Canada: annual summary 1976." 89.
	
Canada, H. a. W. (1981). "Foodborne and waterborne disease in Canada: annual summary 1977." 93.
	
Canada, H. a. W. (1993). "Laboratory reports of human viral and selected non-viral agents in Canada - 1992." Canada Communicable Disease Report 19-22: 188-192.
	not available

Cannon, J. L., E. Papafragkou, et al. (2006). "Surrogates for the study of norovirus stability and inactivation in the environment: aA comparison of murine norovirus and feline calicivirus." J Food Prot 69(11): 2761-5.
	Human noroviruses (NoVs) are the leading cause of food- and waterborne outbreaks of acute nonbacterial gastroenteritis worldwide. As a result of the lack of a mammalian cell culture model for these viruses, studies on persistence, inactivation, and transmission have been limited to cultivable viruses, including feline calicivirus (FCV). Recently, reports of the successful cell culture of murine norovirus 1 (MNV-1) have provided investigators with an alternative surrogate for human NoVs. In this study, we compared the inactivation profiles of MNV-1 to FCV in an effort to establish the relevance of MNV-1 as a surrogate virus. Specifically, we evaluated (i) stability upon exposure to pH extremes; (ii) stability upon exposure to organic solvents; (iii) thermal inactivation; and (iv) surface persistence under wet and dry conditions. MNV-1 was stable across the entire pH range tested (pH 2 to 10) with less than 1 log reduction in infectivity at pH 2, whereas FCV was inactivated rapidly at pH values < 3 and > 9. FCV was more stable than MNV-1 at 56 degrees C, but both viruses exhibited similar inactivation at 63 and 72 degrees C. Long-term persistence of both viruses suspended in a fecal matrix and inoculated onto stainless steel coupons were similar at 4 degrees C, but at room temperature in solution, MNV-1 was more stable than FCV. The genetic relatedness of MNV-1 to human NoVs combined with its ability to survive under gastric pH levels makes this virus a promising and relevant surrogate for studying environmental survival of human NoVs.

Cannon, R. O., J. R. Poliner, et al. (1991). "A multistate outbreak of Norwalk virus gastroenteritis associated with consumption of commercial ice." Journal of Infectious Diseases 164( 5): 860-863.
	Between 19 and 27 September 1987, a cluster of outbreaks of gastrointestinal illness occurred among persons who had attended a museum fund-raiser in Wilmington, Delaware and an intercollegiate football game in Philadelphia. A survey of four groups attending these events showed that 31% (191/614) became ill. Altogether, those who consumed ice were 12 times more likely to experience either vomiting or diarrhea than those who did not (attack rate, 55% vs. 4%, P less than .001). Ice consumed at the events was traced to a manufacturer in southeastern Pennsylvania whose wells had been contaminated when flooded by a nearby creek after a torrential rainfall on 8 September. Of 19 affected persons tested within 1 week of exposure, 13 (68%) had at least a fourfold rise in antibody titer to the Norwalk virus. This report, the first to document an association of contaminated commercial ice with Norwalk gastroenteritis should prompt reassessment of government regulation of the production and distribution of ice. 

Canzonier, W. J. (1971). "Accumulation and elimination of coliphage S-13 by the hard clam, Mercenaria mercenaria." Appl Microbiol 21(6): 1024-31.
	
Caputo, C., A. Forbes, et al. (1999). "Determinants of antibodies to Cryptosporidium infection among gay and bisexual men with HIV infection." Epidemiology and Infection 122(2): 291-297.
	A cross-sectional serosurvey for markers of prior Cryptosporidium infection was conducted among homosexual or bisexual males infected with human immunodeficiency virus (HIV); of 262 individuals approached, 236 (90%) agreed to participate. Serological response to two Cryptosporidium antigens was measured using a Western blot assay. The intensity or detection of serological responses to two Cryptosporidium antigens was not associated with CD4 cell counts or tap water consumption. A number of sexual practices were related to increased serological response for only the 27-kDa marker, including having had sex within the past 2 years, having anal sex and having had a larger number of sex partners during the past 2 years. Attending a spa or sauna was related to serological response to both the 27-kDa and 17-kDa markers. Based on these results, activities related to sexual activity appear to be a significant risk factors for prior Cryptosporidium infection. 

Carducci, A., M. Verani, et al. (2006). "Epidemiological surveillance of human enteric viruses by monitoring of different environmental matrices." Water Sci Technol 54(3): 239-44.
	In the aim of studying possible relations between viruses detected in clinical specimens and the ones found in different environmental matrices, in the period May 2004 to April 2005, the collection of faecal samples from gastroenteritis cases and the monthly monitoring of raw and treated wastewater, river water, seawater and mussels were carried out. The viruses considered for environmental monitoring were adenovirus, rotavirus, enterovirus, norovirus, hepatitis A virus (HAV) and Torque teno virus (TTV): they were searched for with PCR and RT-PCR and confirmed by gene sequencing. Faecal coliforms and somatic coliphages' counts were also determined. The surveillance of case detected 45 positive faecal samples out of 255 (17.6%) while 35 of 56 environmental samples (62.5%) resulted positive for at least one of the considered viruses. The detection of the same viral strain in the faeces of gastroenteritis cases and in water was possible for adenovirus and rotavirus, which were also predominant in environmental matrices; thus they could be considered as a reference for risk assessment.

Carl, M., D. P. Francis, et al. (1983). "Food-borne hepatitis A: recommendations for control." J Infect Dis 148(6): 1133-5.
	
Carninci, P., Y. Nishiyama, et al. (1998). "Thermostabilization and thermoactivation of thermolabile enzymes by trehalose and its application for the synthesis of full length cDNA." Proc Natl Acad Sci U S A 95(2): 520-4.
	The advent of thermostable enzymes has led to great advances in molecular biology, such as the development of PCR and ligase chain reaction. However, isolation of naturally thermostable enzymes has been restricted to those existing in thermophylic bacteria. Here, we show that the disaccharide trehalose enables enzymes to maintain their normal activity (thermostabilization) or even to increase activity at high temperatures (thermoactivation) at which they are normally inactive. We also demonstrate how enzyme thermoactivation can improve the reverse transcriptase, reaction. In fact, thermoactivated reverse transcriptase, which displays full activity even at 60 degrees C, was powerful enough to synthesize full length cDNA without the early termination usually induced by stable secondary structures of mRNA.

Caro, V., S. Guillot, et al. (2001). "Molecular strategy for 'serotyping' of human enteroviruses." J Gen Virol 82(Pt 1): 79-91.
	To explore further the phylogenetic relationships between human enteroviruses and to develop new diagnostic approaches, we designed a pair of generic primers in order to study a 1452 bp genomic fragment (relative to the poliovirus Mahoney genome), including the 3' end of the VP1-coding region, the 2A- and 2B-coding regions, and the 5' moiety of the 2C-coding region. Fifty-nine of the 64 prototype strains and 45 field isolates of various origins, involving 21 serotypes and 6 strains untypable by standard immunological techniques, were successfully amplified with these primers. By determining the nucleotide sequence of the genomic fragment encoding the C-terminal third of the VP1 capsid protein we developed a molecular typing method based on RT-PCR and sequencing. If field isolate sequences were compared to human enterovirus VP1 sequences available in databases, nucleotide identity score was, in each case, highest with the homotypic prototype (74.8 to 89.4%). Phylogenetic trees were generated from alignments of partial VP1 sequences with several phylogeny algorithms. In all cases, the new classification of enteroviruses into five identified species was confirmed and strains of the same serotype were always monophyletic. Analysis of the results confirmed that the 3' third of the VP1-coding sequence contains serotype-specific information and can be used as the basis of an effective and rapid molecular typing method. Furthermore, the amplification of such a long genomic fragment, including non-structural regions, is straightforward and could be used to investigate genome variability and to identify recombination breakpoints or specific attributes of pathogenicity.

Carrique-Mas, J., Y. Andersson, et al. (2003). "A norwalk-like virus waterborne community outbreak in a Swedish village during peak holiday season." Epidemiol Infect 131(1): 737-44.
	An outbreak of gastroenteritis due to Norwalk-like virus (NLV) affecting approximately 500 people occurred in a Swedish ski resort during February-March 2002. Epidemiological investigations were performed on cohorts of schoolchildren, permanent residents and skiers visiting the area. Attack rates were respectively 39.7, 29.9 and 38.5%. Drinking un-boiled water originating from one of the three communal water systems was a significant risk factor for all groups. For schoolchildren, the risk of illness increased with increasing amount of water consumed. Nine of 12 stool samples of patients analysed tested positive for NLV. The water tested negative for indicator bacteria and results of NLV tests were inconclusive. In the absence of microbiological findings, the environmental authorities were reluctant to act based on the epidemiological analysis alone, and intervention was delayed until mid-April, following the discovery of a crack in a sewage pipe 10 m from the well.

Carter, M. J. (2005). "Enterically infecting viruses: pathogenicity, transmission and significance for food and waterborne infection." J Appl Microbiol 98(6): 1354-80.
	
Carter, M. J., I. D. Milton, et al. (1992). "The complete nucleotide sequence of a feline calicivirus." Virology 190(1): 443-8.
	We have determined the complete sequence of a feline calicivirus. The virus genome is 7690 bases long and contains two large open reading frames. Proteins specified by these have similarity to those encoded in the corresponding regions of a candidate calicivirus rabbit hemorrhagic disease virus, but are distinctly different from those specified by another such virus, hepatitis E virus. A third, small open reading frame at the 3' end of the genome is present in both feline and rabbit viruses but is absent from hepatitis E. These findings suggest that the calicivirus family, which consists of a single genus, may require subdivision.

Carter, M. J. and M. M. Willcocks (1996). "The molecular biology of astroviruses." Archives of Virology Supplement 0(12): 277-285.
	Astroviruses (genus Astrovirus) are assigned to a newly established virus family, the Astroviridae. The molecular biology of these agents reveals many features unique amongst the non-enveloped animal viruses and resembles that of members of certain plant virus families. In particular, their possession of a serine protease and use of ribosomal frameshifting to express the RNA polymerase are similar to the luteoviruses. Many aspects of the astrovirus replication strategy are still unclear, but replication may involve a nuclear step and non-structural proteins may influence host cell range.

Casas, I., G. F. Palacios, et al. (2001). "Molecular characterization of human enteroviruses in clinical samples: comparison between VP2, VP1, and RNA polymerase regions using RT nested PCR assays and direct sequencing of products." J Med Virol 65(1): 138-48.
	Three nested RT-PCR assays were developed to permit sensitive typing of enteroviruses directly from clinical samples. These assays amplified short fragments from different genomic regions codifying for three proteins: VP2, VP1, and RNA polymerase. Given that enteroviruses have a high rate of degeneration within target codons among serotypes, the primers used consisted of mixed base and deoxyinosine residues. These techniques detected at 0.03-0.003 TCID50 of prototype Poliovirus 1 and Echovirus 30. They were used to characterize the enteroviral RNA detected in 18 CSF, stool, and throw swab samples and in 8 enterovirus isolates from patients with several syndromes. Phylogenetic analysis in each independent sequenced region grouped the enterovirus into four clusters, enabling genetic classification. A comparative study was performed among the 26 sequences obtained after direct sequencing of products with those available in the nucleotide databases. The efficiency of each assay for enterovirus identification was evaluated by both distance (Clustal) and similarity (M-NW) indices. Comparative results obtained independently in the three regions showed the highest yield of correlation between nucleotide sequences of all prototype serotypes and the analyzed genotypes in the VP1 region (26/26, 100% Clustal; 22/26, 85% M-NW). Conversely, the VP2 region failed to identify some of the circulating enteroviruses (17/26, 65% Clustal; 16/26, 62% M-NW). Using the RNA polymerase region, sequences from samples and isolates were associated with prototype strains whenever these were available (20/21, 95% Clustal; 12/21, 57% M-NW). These assays were useful for molecular identification of enterovirus directly from samples even when isolation was not possible.

Casas, I., L. Powell, et al. (1995). "New method for the extraction of viral RNA and DNA from cerebrospinal fluid for use in the polymerase chain reaction assay." J Virol Methods 53(1): 25-36.
	A new, rapid, and simple method for the isolation of either RNA or DNA from cerebrospinal fluid samples for subsequent amplification by specific polymerase chain reaction (PCR) assays is described. The technique involves a single extraction with a guanidinium thiocyanate acid (GuSCN) buffer, and does not require the use of organic solvents. Applied to the recovery of enteroviral RNA, herpes simplex virus (HSV) and Varicella-zoster virus (VZV) DNAs the method has proved to be of equivalent or better efficiency than established methods of nucleic acid separation but is less laborious and time consuming. The simplicity of the procedure permits the processing of large numbers of samples and the use of a single preparative method for either RNA or DNA PCR makes it an attractive method for the routine laboratory.

Casas, I., A. Tenorio, et al. (1997). "Detection of enteroviral RNA and specific DNA of herpesviruses by multiplex genome amplification." J Virol Methods 66(1): 39-50.
	A reverse transcription (RT) multiplex polymerase chain reaction (PCR) assay was developed to allow rapid, sensitive and simultaneous detection of enteroviral RNA and herpesviral DNA specific sequences in a single tube. The method involves a reverse transcription step followed by a multiplex nested PCR in which the combination of primers amplifies cDNA from enteroviruses and specific herpesviruses DNA. Nested amplification utilises primers designed to anneal into the amplification product from the first reaction. Individual viruses were then detected and differentiated by the size of their PCR products determined using ethidium bromide stained agarose gels. To exclude false negatives due to sample inhibitors an internal amplification control, a cloned fragment of DNA from Pseudorabies virus (PRV DNA) was included in the reaction mixture. Detection levels between 0.01 and 0.001 TCID50 of prototype strains of Polio and Coxsackie type B viruses and between 1 and 100 molecules of cloned-DNA of herpesviruses prototype strains were achieved. The RT multiplex PCR method proved capable of detecting enteroviral RNA or herpesviral DNA in cerebro spinal fluid (CSF) samples from patients with aetiologically well characterized encephalitis or aseptic meningitis.

Casas, N. and E. Sunen (2001). "Detection of enterovirus and hepatitis A virus RNA in mussels (Mytilus spp.) by reverse transcriptase-polymerase chain reaction." J Appl Microbiol 90(1): 89-95.
	AIMS: A simple and effective method of concentrating and purifying enteric viruses from mussel samples to be detected by nucleic acid extraction reverse transcriptase-polymerase chain reaction (RT-PCR) has been evaluated. METHODS AND RESULTS: Seeded mussels were processed by alkaline elution, polyethylene glycol (PEG) precipitation, solvent extraction and PEG precipitation. Final concentrates were assayed by infectivity and RT-PCR after nucleic acid extraction. Two RNA extraction methods were comparatively evaluated for removing inhibitory substances: guanidinium thiocyanate extraction and Purescripttrade mark RNA isolation. Both procedures removed most inhibitors allowing the detection of viral RNA at inoculum levels as low as 4 pfu g(-1) for poliovirus type 1 and 1.8-18 most probable number of cytopathogenic units g(-1) for HAV. When inhibitors remained, they were efficiently removed by Sephadex column chromatography before RNA extraction. CONCLUSION: The described method is effective for the detection of enteric viruses in mussels by RT-PCR. The use of Purescripttrade mark RNA isolation makes the method faster, safer and very easy to perform.

Casas, N. and E. Sunen (2002). "Detection of enteroviruses, hepatitis A virus and rotaviruses in sewage by means of an immunomagnetic capture reverse transcription-PCR assay." Microbiol Res 157(3): 169-75.
	An immunomagnetic capture reverse transcription-PCR (IMC-RT-PCR) assay was evaluated to recover and detect enteric viruses in sewage and to remove PCR inhibitors. The procedure was applied along with a simple sample processing consisting of an initial separation of solids followed by polyethylen glycol precipitation and solvent extraction. This procedure reduced sample volumes by about 65-fold without eliminating RT-PCR inhibitors. Paramagnetic beads coupled to pooled human immunoglobulins were used to simultaneously capture poliovirus 1 (PV-1) and hepatitis A virus (HAV) from seeded sewage concentrates. The IMC was efficient in removing PCR inhibitors and in further reducing sample volumes by approximately 10-fold allowing the analysis of 6-7 ml of sewage sample per RT-PCR reaction. The detection limits of IMC-RT-PCR from seeded concentrates were 0.1-1 PFU for PV-1 and 1 MPNCU for HAV. The described procedure could be applied successfully for the detection of enteroviruses, HAV and rotaviruses in field sewage samples.

Cashdollar, J. L. and D. R. Dahling (2006). "Evaluation of a method to re-use electropositive cartridge filters for concentrating viruses from tap and river water." J Virol Methods 132(1-2): 13-7.
	Electropositively charged filters are frequently used for concentrating enteric viruses from large volumes of water. A major disadvantage to the use of these filters, however, is that they are not cost-effective. At US$ 150-180 per filter, routine viral monitoring of water is cost-prohibitive. This study describes the development of a method which allows a filter to be used up to three times, achieving comparable recoveries to new filters. Zetapor 1MDS and N66 Posidyne electropositive filters were tested. The method was analyzed using tap water and Ohio River water that was spiked with poliovirus. Tap water recoveries averaged 32% for new filters, 30% for filters used twice, and 38% for filters used three times. River water recoveries averaged 68% for new filters, 83% for filters used twice, and 100% for filters used three times. RT-PCR and dot-blot hybridization were performed on sample concentrates to ensure that all viral nucleic acid from the previous test had been removed from the filters by the treatment process.

Casteel, M. J., C. E. Schmidt, et al. (2008). "Chlorine disinfection of produce to inactivate hepatitis A virus and coliphage MS2." Int J Food Microbiol 125(3): 267-73.
	Disinfection of produce is principally used to inactivate spoilage microbes and may also reduce the risk of consumer exposure to enteric pathogens. However, the rate and extent of enteric virus inactivation by free chlorine on produce has not been adequately characterized. Experiments were performed to determine the kinetics of free chlorine inactivation of hepatitis A virus (HAV) and the indicator virus coliphage MS2 on strawberries (SBs), cherry tomatoes (CTs), and head lettuce (HL). The oxidant demand of these produce items also was determined. When produce items were exposed to approximately 20 parts per million (ppm) solution of free chlorine for 5-10 min, HAV and MS2 were inactivated by 90-99% and in some cases virus inactivation was > or =99%. Exposure of strawberries to approximately 200 ppm free chlorine resulted in more rapid and extensive inactivation of both viruses. The produce items tested in this study exhibited a demand for chlorine which varied by produce type, and chlorine residuals declined over time. These results demonstrate the potential for chlorine to reduce the levels of infectious viruses on different produce types, but adequate contact time and chlorine residual are required to achieve maximum virus inactivation. The difference in chlorine demand between SBs, CTs, and HL suggests that varying disinfection practices are needed for the wide variety of processed fruits and vegetables. The inactivation kinetics of MS2 and HAV were similar, suggesting that MS2 and perhaps other similar bacterial viruses may be used as process indicators and surrogates for determining the disinfection efficacy of produce in the laboratory or in actual practice.

Castillo, G., R. Thiers, et al. (1988). "Coliphage association with coliform indicators: a case study in Chile."??? 3: 535-550.
	This paper summarizes the results obtained from an International Developement Research Centre (IDRC), Ottwa, Canada, funded study to evaluate the potential of using coliphage as an indicator of water quality. Raw water sample data indicated that the A-1 test combined with the coliphage test would make an excellent screening program for health hazards in these water. The superiority of the Presence/Absence test for detecting microbobial health hazards in potable water was readily shown, while the H2S paper strip techinque was found to be equally efficient for testing potable waters as traditional coliform water quality indicators.

Caul, E. O. (1994). "Small round structured viruses: airborne transmission and hospital control." Lancet 343(8908): 1240-2.
	
Caul, E. O. (1996). "Viral gastroenteritis: small round structured viruses, caliciviruses and astroviruses. Part I. The clinical and diagnostic perspective." J Clin Pathol 49(11): 874-80.
	
Caul, E. O. and H. Appleton (1982). "The electron microscopical and physical characteristics of small round human fecal viruses: an interim scheme for classification." Journal of Medical Virology 9(4): 257-65.
	Many of the small round human fecal viruses implicated in outbreaks of nonbacterial gastroenteritis have been collected together and examined under the electron microscope. Negatively stained preparations without the addition of antibody were used so that the surface morphology of the virus particles remained clearly visible. It was apparent that several viruses, previously thought to be simply antigenic variants within the Norwalk group of viruses, show distinct morphological differences and quite clearly belong to other virus groups. By comparing the features of all the viruses examined in this study, both with each other and with standard cell culture strains of enterovirus, parvovirus, and calicivirus, it has been possible to propose an interim classification scheme, based primarily on the morphological appearance of the particles and supported by estimations of size and buoyant density.

Caul, E. O., C. Ashley, et al. (1979). ""Norwalk"-like particles in the epidemic gastroenteritis in the U.K." Lancet 2(8155): 1292.
	
Caul, E. O., C. R. Ashley, et al. (1977). "Recognition of human enteric coronaviruses by electron microscopy." Med Lab Sci 34(3): 259-63.
	
Caul, E. O. and S. I. Egglestone (1977). "Further studies on human enteric coronaviruses." Arch Virol 54(1-2): 107-17.
	Comparisons were made between human enteric coronaviruses and the enteric coronaviruses of pigs and calves by negative staining. Examination of human intestinal organ culture fluids at various time intervals after inoculation with the human enteric coronavirus showed increasing numbers of particles in the fluids. Thin sections of the columnar epithelial cells of these explants showed a number of features consistent with the replication of known human and animal coronaviruses. Virus particles found in thin sections had a mean diameter of 68 nm. In addition, a structure was found in thin sections which has not been described previously. This structure may represent the viral nucleocapsid.

Caul, E. O., N. J. Sellwood, et al. (1993). "Outbreaks of gastroenteritis associated with SRSVs." Public Health Library Service, UK - Microbiology Digest 10: 2-8.
	
CDC (1999). "Prevention of hepatitis A through active or passive immunization: Recommendations of the Advisory Committee on Immunization Practices (ACIP)." MMWR. Morbidity and Mortality Weekly Report 48(RR-12): 1-37.
	Routine vaccination of children is the most effective way to reduce hepatitis A incidence nationwide over time. Since licensure of hepatitis A vaccine in 1995, this strategy has been implemented incrementally, starting with the recommendation of the Advisory Committee on Immunization Practices (ACIP) in 1996 to vaccinate children living in communities with the highest rates of infection and disease. These updated recommendations represent the next phase of this hepatitis A immunization strategy. Vaccination of children living in states and communities with consistently elevated rates of hepatitis A will provide protection from disease and is expected to reduce the overall incidence of hepatitis A. This report updates the ACIP's 1996 recommendations on the prevention of hepatitis A through immunization (MMWR 1996;45:[No. RR-151) and includes a) new data about the epidemiology of hepatitis A; b) recent findings about the effectiveness of community-based hepatitis A vaccination programs; and c) recommendations for the routine vaccination of children in states, counties, and communities with rates that are twice the 1987-1997 national average or greater (i.e., > or = 20 cases per 100,000 population) and consideration of routine vaccination of children in states, counties, and communities with rates exceeding the 1987-1997 national average (i.e., > or = 10 but <20 cases per 100,000 population). Unchanged in this report are previous recommendations regarding the vaccination of persons in groups at increased risk for hepatitis A or its adverse consequences and recommendations regarding the use of immune globulin for protection against hepatitis A.

CDC (1999). "Summary of Notifiable Diseases, United States, 1998." MMWR. Morbidity and Mortality Weekly Report 48(53): 1-104.
	The MMWR Summary of Notifiable Diseases, United States, 1998 contains summary tables of the official statistics for the reported occurrence of nationally notifiable diseases in the United States for 1998. These statistics are collected and compiled from reports to the National Notifiable Diseases Surveillance System (NNDSS), which is operated by CDC in collaboration with the Council of State and Territorial Epidemiologists (CSTE).

CDC (2001). "Norwalk-like viruses: Public health consequences and outbreak management." MMWR. Morbidity and Mortality Weekly Report 50(RR-09): 1-18.
	
Chadwick, P. R., G. Beards, et al. (2000). "Management of hospital outbreaks of gastro-enteritis due to small roundstructured viruses." J Hosp Infect 45(1): 1-10.
	Small round structured viruses (SRSVs, Norwalk-like viruses, NLVs) are the most common cause of outbreaks of gastro-enteritis in hospitals and also cause outbreaks in other settings such as schools, hotels, nursing homes and cruise ships. Hospital outbreaks often lead to ward closure and major disruption in hospital activity. Outbreaks usually affect both patients and staff, sometimes with attack rates in excess of 50%. For this reason, staff shortages can be severe, particularly if several wards are involved at the same time. SRSVs may be spread by several routes: faecal-oral; vomiting/aerosols; food and water. Viruses may be introduced into the ward environment by any of these routes and then propagated by person-to-person spread. In an outbreak setting, the diagnosis can usually be made rapidly and confidently on clinical and epidemiological grounds, particularly if vomiting is a prominent symptom. By the time an SRSV outbreak has been recognized at ward level, most susceptible individuals will have been exposed to the virus and infection control efforts must prioritize the prevention of spread of infection to other clinical areas bycontainment of infected/exposed individuals (especially the prevention of patient and staff movements to other areas), hand-hygiene and effective environmental decontamination.This report of the Public Health Laboratory Service Viral Gastro-enteritis Working Group reviews the epidemiology of outbreaks of infection due to SRSVs and makes recommendations for their management in the hospital setting. The basic principles which underpin these recommendations will also be applicable to the management of some community-based institutional outbreaks.

Chadwick, P. R. and R. McCann (1994). "Transmission of a small round structured virus by vomiting during a hospital outbreak of gastroenteritis." J Hosp Infect 26(4): 251-9.
	An outbreak of gastroenteritis due to a small round structured virus (SRSV) (Norwalk-like virus) occurred in an elderly care unit, affecting a total of 126 patients and staff. The outbreak caused major disruption to the provision of health care services by the unit over a 3-week period. Following the outbreak a study was undertaken to explore risk factors for acquisition of SRSV infection by health care workers on the unit. Exposure to patients nearby who were vomiting and the number of close contacts with ill patients were significantly related to the risk of developing gastroenteritis (P < 0.05). No significant increase in risk of developing gastroenteritis was found in nurses who cleaned vomit or faeces from affected patients. The findings suggest that aerosolization of vomit was of major importance in transmission of infection during the outbreak; the implications for infection control are discussed.

Chadwick, P. R., M. Walker, et al. (1994). "Airborne transmission of a small round structured virus." Lancet 343(8890): 171.
	
Chalmers, J. W. T. and J. H. McMillan (1995). "An outbreak of viral gastroenteritis associated with adequately prepared oysters." Epidemiology and Infection 115(1): 163-167.
	Over Christmas 1993, an outbreak of food poisoning occurred among guests in a hotel in South West Scotland. Evidence from a cohort study strongly suggested that raw oysters were the vehicle for infection, probably due to a Small Round Structured Virus (SRSV). Detailed enquiry about the source and preparation of the oysters revealed no evidence of any unsafe handling at any stage in the food chain, nor any evidence of bacterial contamination. It is suggested that the present standards of preparation and monitoring are inadequate to protect the consumer, and that bacteriophage monitoring may be a useful method of screening for viral contamination in future.

Chan, K. H., L. L. Poon, et al. (2004). "Detection of SARS coronavirus in patients with suspected SARS." Emerg Infect Dis 10(2): 294-9.
	Cases of severe acute respiratory syndrome (SARS) were investigated for SARS coronavirus (SARS-CoV) through RNA tests, serologic response, and viral culture. Of 537 specimens from patients in whom SARS was clinically diagnosed, 332 (60%) had SARS-CoV RNA in one or more clinical specimens, compared with 1 (0.3%) of 332 samples from controls. Of 417 patients with clinical SARS from whom paired serum samples were available, 92% had an antibody response. Rates of viral RNA positivity increased progressively and peaked at day 11 after onset of illness. Although viral RNA remained detectable in respiratory secretions and stool and urine specimens for >30 days in some patients, virus could not be cultured after week 3 of illness. Nasopharyngeal aspirates, throat swabs, or sputum samples were the most useful clinical specimens in the first 5 days of illness, but later in the illness viral RNA could be detected more readily in stool specimens.

Chan MCW, S. J., Lam RKY, Chan PKS, Lee NLS, Lai RWM, et al. (2006). " Fecal viral load and norovirus-associated gastroenteritis." Emerg Infect Dis [serial on the Internet]. 12(8): 1278-1280.
	
Chan, T. Y. (1995). "Shellfish-borne illnesses. A Hong Kong perspective." Trop Geogr Med 47(6): 305-7.
	This article provides an overview of the spectrum of infectious and toxic illnesses that may occur following the consumption of contaminated shellfish in Hong Kong. These include hepatitis A, hepatitis E, infections due to vibrio species, paralytic shellfish poisoning, neurotoxic shellfish poisoning and heavy metal poisoning. Possible preventive measures are discussed.

Chancellor, D. D., S. Tyagi, et al. (2006). "Green onions: potential mechanism for hepatitis A contamination." J Food Prot 69(6): 1468-72.
	The largest documented foodborne hepatitis A outbreak in U.S. history occurred in November 2003. The source of that outbreak was green onions from a farm in Mexico. Two biomarkers were used to determine ways in which hepatitis A virus (HAV) can contaminate onions. Fluorescent microspheres (1.0 to 10 microm) and HAV vaccine were placed on the soil and the surfaces of pot-grown onions and in the liquid medium of hydroponically cultivated onions. Reverse transcription PCR (RT-PCR) was used to identify HAV RNA. Microspheres were found on the outside and inside of the pot-grown onions for up to 60 days. RT-PCR revealed HAV RNA from the vaccine in well-washed green onions. In the hydroponically grown onions, microspheres were found throughout the onion after only 1 day. RT-PCR also revealed HAV RNA inside the hydroponically grown onions. Both biomarkers support the hypothesis that HAV can contaminate the inside of the growing onion and can be taken up intracellularly through the roots. Once inside, the particles are impossible to remove by cleaning.

Chandler, D. P., J. R. Stults, et al. (2000). "Affinity purification of DNA and RNA from environmental samples with peptide nucleic acid clamps." Appl Environ Microbiol 66(8): 3438-45.
	Bispeptide nucleic acids (bis-PNAs; PNA clamps), PNA oligomers, and DNA oligonucleotides were evaluated as affinity purification reagents for subfemtomolar 16S ribosomal DNA (rDNA) and rRNA targets in soil, sediment, and industrial air filter nucleic acid extracts. Under low-salt hybridization conditions (10 mM NaPO(4), 5 mM disodium EDTA, and 0.025% sodium dodecyl sulfate [SDS]) a PNA clamp recovered significantly more target DNA than either PNA or DNA oligomers. The efficacy of PNA clamps and oligomers was generally enhanced in the presence of excess nontarget DNA and in a low-salt extraction-hybridization buffer. Under high-salt conditions (200 mM NaPO(4), 100 mM disodium EDTA, and 0.5% SDS), however, capture efficiencies with the DNA oligomer were significantly greater than with the PNA clamp and PNA oligomer. Recovery and detection efficiencies for target DNA concentrations of > or =100 pg were generally >20% but depended upon the specific probe, solution background, and salt condition. The DNA probe had a lower absolute detection limit of 100 fg of target (830 zM [1 zM = 10(-21) M]) in high-salt buffer. In the absence of exogenous DNA (e.g., soil background), neither the bis-PNA nor the PNA oligomer achieved the same absolute detection limit even under a more favorable low-salt hybridization condition. In the presence of a soil background, however, both PNA probes provided more sensitive absolute purification and detection (830 zM) than the DNA oligomer. In varied environmental samples, the rank order for capture probe performance in high-salt buffer was DNA > PNA > clamp. Recovery of 16S rRNA from environmental samples mirrored quantitative results for DNA target recovery, with the DNA oligomer generating more positive results than either the bis-PNA or PNA oligomer, but PNA probes provided a greater incidence of detection from environmental samples that also contained a higher concentration of nontarget DNA and RNA. Significant interactions between probe type and environmental sample indicate that the most efficacious capture system depends upon the particular sample type (and background nucleic acid concentration), target (DNA or RNA), and detection objective.

Chandler, D. P., C. A. Wagnon, et al. (1998). "Reverse transcriptase (RT) inhibition of PCR at low concentrations of template and its implications for quantitative RT-PCR." Appl Environ Microbiol 64(2): 669-77.
	Numerous instances of reverse transcriptase (RT) inhibition of the PCR were observed while developing nonquantitative uncoupled RT-PCR techniques for detecting nitrogenase and ammonia monooxygenase gene expression in situ. The inhibitory effect of RT on the PCR was removed with increasing template concentrations beyond 10(5) to 10(6) copies. Including T4 gene 32 protein during the reverse transcription phase of the RT-PCR reaction increased the RT-PCR product yield by as much as 483%; if gene 32 protein was introduced after reverse transcription but prior to the PCR phase, no improvement in product yield was observed. Addition of 1 microgram of exogenous calf thymus DNA or yeast tRNA did little to relieve RT inhibition of the PCR on both genomic DNA and mRNA templates. These results suggest that RT inhibition of the PCR is mediated through direct interaction with the specific primer-template combination (DNA and RNA) and point to specific assay modifications for estimating the extent of RT inhibition and counteracting some of the inhibitory effect. Furthermore, the working hypothesis of RT inhibition below a 10(5) to 10(6) copy threshold has important implications for quantitative RT-PCR studies. In particular, competitive, quantitative RT-PCR systems will consistently underestimate the actual RNA concentration. Hence, enumerations of RNA templates below 10(5) to 10(6) copies will be relative to an internal standard and will not be an absolute measure of RNA abundance in situ.

Chang, J. C., S. F. Ossoff, et al. (1985). "UV inactivation of pathogenic and indicator microorganisms." Applied and Environmental Microbiology 49(6): 1361-5.
	Survival was measured as a function of the dose of germicidal UV light for the bacteria Escherichia coli, Salmonella typhi, Shigella sonnei, Streptococcus faecalis, Staphylococcus aureus, and Bacillus subtilis spores, the enteric viruses poliovirus type 1 and simian rotavirus SA11, the cysts of the protozoan Acanthamoeba castellanii, as well as for total coliforms and standard plate count microorganisms from secondary effluent. The doses of UV light necessary for a 99.9% inactivation of the cultured vegetative bacteria, total coliforms, and standard plate count microorganisms were comparable. However, the viruses, the bacterial spores, and the amoebic cysts required about 3 to 4 times, 9 times, and 15 times, respectively, the dose required for E. coli. These ratios covered a narrower relative dose range than that previously reported for chlorine disinfection of E. coli, viruses, spores, and cysts.

Chang, K. H., P. Auvinen, et al. (1989). "The nucleotide sequence of coxsackievirus A9; implications for receptor binding and enterovirus classification." J Gen Virol 70 ( Pt 12): 3269-80.
	The complete nucleotide sequence of the genome of coxsackievirus A9 (CAV-9) has been determined from cDNA cloned in Escherichia coli. Excluding the 3' poly(A) stretch, the RNA genome is 7452 nucleotides long and encodes a single polyprotein of 2201 amino acids. Comparison of the nucleotide and predicted amino acid sequences with those of the coxsackieviruses B1, B3 and B4 reveals a surprising degree of homology, with overall amino acid homologies of 86.9%, 86.2% and 87.0%, respectively. In contrast, there is much less homology to another coxsackie A virus, CAV-21, 60.4% overall amino acid homology. This demonstrates the high degree of diversity within the CAV group and indicates that the current classification does not directly correlate with molecular genetic properties. One major feature of CAV-9 is an insertion, relative to all other enteroviruses sequenced to date, which is located at the C terminus of VP1, and includes an arginine-glycine-aspartic acid tripeptide. Such sequences in a number of other proteins are known to have activity in promoting attachment to cell receptors and the implications for CAV-9 receptor binding are discussed.

Chang, K. H., C. Day, et al. (1992). "The nucleotide sequences of wild-type coxsackievirus A9 strains imply that an RGD motif in VP1 is functionally significant." J Gen Virol 73 ( Pt 3): 621-6.
	We have shown previously that, compared to other enteroviruses, the coxsackievirus A9 (CAV-9) prototype strain, Griggs, contains a C-terminal extension to the capsid protein VP1 and that within this extension there is an RGD (arginine-glycine-aspartic acid) motif. To determine whether these features are found in other CAV-9 strains and therefore analyse whether they are likely to be functionally important, we have determined the nucleotide sequence of the appropriate region from five strains, isolated over a 25 year period. The results indicate that there is considerable diversity between the strains and there is little correlation between nucleotide sequence identity and date of isolation. All isolates exhibit the VP1 extension and although its amino acid sequence is otherwise variable, the RGD motif is common to all. This conservation of sequence, within a region which can otherwise vary, implies that the RGD sequence must be functionally significant. The VP1 extension shows similarity to sequences found in foot-and-mouth-disease virus strains and to part of the precursor of the cellular protein, human transforming growth factor beta, and the possible significance of these observations is discussed.

Chang, K. O., P. R. Nielsen, et al. (1999). "Dual infection of gnotobiotic calves with bovine strains of group A and porcine-like group C rotaviruses influences pathogenesis of the group C rotavirus." J Virol 73(11): 9284-93.
	There is serological evidence that bovine group C rotaviruses exist in the United States, but there are no reports of their isolation. Ninety fecal samples from calves with diarrhea, 81 samples from adult cows with diarrhea (winter dysentery), and 20 fecal samples from healthy adult cows were tested for group C rotaviruses by polyacrylamide gel electrophoresis, immune electron microscopy, and reverse transcription-PCR (RT-PCR). Three samples from adult cow diarrhea cases were positive only by RT-PCR, and a group C rotavirus was isolated from a positive sample in monkey kidney (MA104) cells (WD534tc/C). Genetically and serologically, the WD534tc/C strain was more closely related to the Cowden porcine group C strain than to the Shintoku bovine strain. Because the original cow feces also contained a group A rotavirus (detected after passage in cell culture), we hypothesized that such dual-rotavirus infections might play a role in the pathogenesis and host adaptation of rotaviruses. Thus, we examined the pathogenesis of WD534tc/C alone or combined with virulent (IND/A) or attenuated (NCDV/A) bovine group A rotaviruses in gnotobiotic calves. WD534tc/C alone induced diarrhea without (or with limited) virus shedding in inoculated calves (n = 3). In contrast, all calves coinfected with WD534tc/C and IND/A (n = 2) developed diarrhea and shed both viruses, whereas calves coinfected with WD534tc/C and NCDV/A (n = 3) developed diarrhea but did not shed either virus. Infection with WD534tc/C or NCDV/A alone caused only mild villous atrophy (jejunum and/or ileum), whereas dual infection with both viruses induced lesions throughout the small intestine. Although IND/A alone caused villous atrophy, more-widespread small intestinal lesions occurred in calves coinfected with WD534tc/C and IND/A. In conclusion, coinfection of calves with group A rotaviruses enhanced fecal shedding of a bovine group C rotavirus and the extent of histopathological lesions in the small intestines. Thus, our findings suggest a potential nov