Detection of sapoviruses and noroviruses in an outbreak of gastroenteritis linked genetically to shellfish

Improvement of nested reverse transcription-polymerase chain reaction (RT-PCR) with high specificity and sensitivity detection of sapovirus in food matrix

Sapovirus (SaV) is a causative agent of human gastroenteritis in both community outbreaks and sporadic cases worldwide. Shellfish accumulate a variety of pathogens during filter feeding. In particular, the contamination of shellfish by SaV has caused several outbreaks. As reported previously, nested RT-PCR (nRT-PCR) has been widely used in clinical samples, but has not proven suitable for food samples, such as oysters. This study aimed to identify a primer set for the detection of SaV with high specificity and sensitivity in food samples. To accomplish this, primers were improved in RNA-dependent RNA polymerase (RdRp) regions of SaV whole genome sequences. The sensitivity of the improved nRT-PCR was 100-1000 times higher than that of previous nRT-PCR and > 10 times higher than that of the previous real-time RT-PCR assay. Notably, cross-reaction with other viruses or food matrices was not observed by the specificity test. This study improved the reliable primer set to detect SaV in various food matrices with high sensitivity.

Sources, fates and treatment strategies of typical viruses in urban sewage collection/treatment systems: A review

The ongoing coronavirus pandemic (COVID-19) throughout the world has severely threatened the global economy and public health. Due to receiving severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) from a wide variety of sources (e.g., households, hospitals, slaughterhouses), urban sewage treatment systems are regarded as an important path for the transmission of waterborne viruses. This review presents a quantitative profile of the concentration distribution of typical viruses within wastewater collection systems and evaluates the influence of different characteristics of sewer systems on virus species and concentration. Then, the efficiencies and mechanisms of virus removal in the units of wastewater treatment plants (WWTPs) are summarized and compared, among which the inactivation efficiencies of typical viruses by typical disinfection approaches under varied operational conditions are elucidated. Subsequently, the occurrence and removal of viruses in treated effluent reuse and desalination, as well as that in sewage sludge treatment, are discussed. Potential dissemination of viruses is emphasized by occurrence via aerosolization from toilets, the collection system and WWTP aeration, which might have a vital role in the transmission and spread of viruses. Finally, the frequency and concentration of viruses in reclaimed water, the probability of infection are also reviewed for discussing the potential health risks.

Prevalence and Genetic Characterisation of Human Sapovirus from Children with Diarrhoea in the Rural Areas of Vhembe District, South Africa, 2017-2020

Diarrhoeal disease is considered an important cause of morbidity and mortality in developing areas, and a large contributor to the burden of disease in children younger than five years of age. This study investigated the prevalence and genogroups of human sapovirus (SV) in children ≤5 years of age in rural communities of Vhembe district, South Africa. Between 2017 and 2020, a total of 284 stool samples were collected from children suffering with diarrhoea (n = 228) and from children without diarrhoea (n = 56). RNA extraction using Boom extraction method, and screening for SV using real-time PCR were done in the lab. Positive samples were subjected to conventional RT-PCR targeting the capsid fragment. Positive sample isolates were genotyped using Sanger sequencing. Overall SV were detected in 14.1% (40/284) of the stool samples (16.7% (38/228) of diarrhoeal and 3.6% (2/56) of non-diarrhoeal samples). Significant correlation between SV positive cases and water sources was noted. Genogroup-I was identified as the most prevalent strain comprising 81.3% (13/16), followed by SV-GII 12.5% (2/16) and SV-GIV 6.2% (1/16). This study provides valuable data on prevalence of SV amongst outpatients in rural and underdeveloped communities, and highlights the necessity for further monitoring of SV circulating strains as potential emerging strains.

Prevalence and genetic diversity of human sapovirus associated with sporadic acute gastroenteritis in South China from 2013 to 2017

Human sapovirus (SaV) is an important viral agent for acute diarrhea worldwide, but timely prevalence data of human SaV in South China are still lacking. In this study, a 4-year surveillance was conducted to characterize the prevalence and genetic characteristics of the circulating SaV associated with sporadic diarrhea in South China. From November 2013 to October 2017, 569 fecal samples from patients with acute diarrhea were collected. SaV was detected in 11 samples with a positive rate of 1.93%. Three human genogroups of GI, GII, and GIV were identified, including five GI.1 strains, three GI.2 strains, one GI.3 strain, one GII.8 strain, and one GIV strain. Furthermore, multiple alignments of complete capsid protein VP1 genes of five local GI.1 strains and other available GI.1 strains in GenBank were performed. Average pairwise identities were calculated at 95.33% and 99.36% at nucleotide and amino acid levels, and only six variable amino acid sites were found during its 36-years' evolution process. GI.1 strains could be further phylogenetically divided into four clusters with an approximate temporal evolution pattern, and local strains belonged to Cluster-d with other four strains from China and Japan. In summary, SaV was identified as an etiological agent responsible for sporadic gastroenteritis in Guangzhou with a low prevalence rate as in other Chinese cities, but its high genetic diversity suggested the necessity of continuous SaV surveillance in the future.

Cockles and mussels, alive, alive, oh-The role of bivalve molluscs as transmission vehicles for human norovirus infections

Human noroviruses are recognized as the leading worldwide cause of sporadic and epidemic viral gastroenteritis, causing morbidity and mortality in impoverished developing countries and engendering enormous economic losses in developed countries. Transmitted faecal-orally, either via person-to-person contact, or by consumption of contaminated foods or water, norovirus outbreaks are often reported in institutional settings or in the context of communal dining. Bivalve molluscs, which accumulate noroviruses via filter feeding and are often eaten raw or insufficiently cooked, are a common food vehicle implicated in gastroenteritis outbreaks. The involvement of bivalve molluscs in norovirus outbreaks and epidemiology over the past two decades are reviewed. The authors describe how their physiology of filter feeding can render them concentrated vehicles of norovirus contamination in polluted environments and how high viral loads persist in molluscs even after application of depuration practices and typical food preparation steps. The global prevalence of noroviruses in bivalve molluscs as detected by different monitoring efforts is determined and the various methods currently utilized for norovirus extraction and detection from bivalve matrices described. An overview of gastroenteritis outbreaks affirmatively associated with norovirus-contaminated bivalve molluscs as reported in the past 18 years is also provided. Strategies for risk reduction in shellfish contamination and subsequent human infection are discussed.

Broadly reactive real-time reverse transcription-polymerase chain reaction assay for the detection of human sapovirus genotypes

Sapoviruses are associated with acute gastroenteritis. Human sapoviruses are classified into four distinct genogroups (GI, GII, GIV, and GV) based on their capsid gene sequences. A TaqMan probe-based real-time reverse transcription-polymerase chain reaction (RT-PCR) assay that detects the representative strains of these four genogroups is widely used for screening fecal specimens, shellfish, and environmental water samples. However, since the development of this test, more genetically diverse sapovirus strains have been reported, which are not detectable by the previously established assays. In this study, we report the development of a broader-range sapovirus real-time RT-PCR assay. The assay can detect 2.5 × 10⁷ and 2.5 × 10 ¹ copies of sapovirus and therefore is as sensitive as the previous test. Analysis using clinical stool specimens or synthetic DNA revealed that the new system detected strains representative of all the 18 human sapovirus genotypes: GI.1-7, GII.1-8, GIV.1, and GV.1, 2. No cross-reactivity was observed against other representative common enteric viruses (norovirus, rotavirus, astrovirus, and adenovirus). This new assay will be useful as an improved, broadly reactive, and specific screening tool for human sapoviruses.

Prevalence of Human Sapovirus in Low and Middle Income Countries

Background

Sapovirus (SV) infection is a public health concern which plays an important role in the burden of diarrhoeal diseases, causing acute gastroenteritis in people of all ages in both outbreaks and sporadic cases worldwide.

Objective/Study Design

The purpose of this report is to summarise the available data on the detection of human SV in low and middle income countries. A systematic search on PubMed and ScienceDirect database for SV studies published between 2004 and 2017 in low and middle income countries was done. Studies of SV in stool and water samples were part of the inclusion criteria.

Results

From 19 low and middle income countries, 45 published studies were identified. The prevalence rate for SV was 6.5%. A significant difference (P=0) in SV prevalent rate was observed between low income and middle income countries. Thirty-three (78.6%) of the studies reported on children and 8 (19%) studies reported on all age groups with diarrhoea. The majority (66.7%) of studies reported on hospitalised patients with acute gastroenteritis. Sapovirus GI was shown as the dominant genogroup, followed by SV-GII.

Conclusion

The detection of human SV in low and middle income countries is evident; however the reports on its prevalence are limited. There is therefore a need for systematic surveillance of the circulation of SV, and their role in diarrhoeal disease and outbreaks, especially in low and middle income countries.

First Complete Genome Sequences of Human Sapovirus Strains Classified as GI.3, GI.4, GI.6, GI.7, and GII.7

We report here the first complete genome sequences of genotype GI.3, GI.4, GI.6, GI.7, and GII.7 sapovirus strains, detected from fecal samples of acute gastroenteritis patients. Complete or nearly complete genome sequences of all 18 genotypes of human sapoviruses are now available for phylogenetic analysis and primer design.

An overview of 20 years of studies on the prevalence of human enteric viruses in shellfish from Galicia, Spain

Galicia (NW Spain) has 1490 km of coastline, and its particular topography, characterized by the presence of fiord-like inlets, called rías, with an important primary production, makes this region very favourable for shellfish growth and culture. In fact, Galicia is one of the most important mussel producers in the world. Due to its proximity to cities and villages and the anthropogenic activities in these estuaries, and despite the routine official controls on the bivalve harvesting areas, contamination with material of faecal origin is sometimes possible but, current regulation based on Escherichia coli as an indicator micro-organism has been revealed as useful for bacterial contaminants, this is not the case for enteric viruses. The aim of this review is to offer a picture on the situation of different harvesting areas in Galicia, from a virological standpoint. A recompilation of results obtained in the last 20 years is presented, including not only the data for the well-known agents norovirus (NoV) and hepatitis A virus (HAV) but also data on emerging viral hazards, including sapovirus (SaV), hepatitis E virus (HEV) and aichivirus (AiV). Epidemiological differences related to diverse characteristics of the harvesting areas, viral genotype distribution or epidemiological links between environmental and clinical strains will also be presented and discussed. The presentation of these historical data all together could be useful for future decisions by competent authorities for a better management of shellfish growing areas.

Genetic diversity and intergenogroup recombination events of sapoviruses detected from feces of pigs in Japan

Sapoviruses (SaV) are enteric viruses infecting humans and animals. SaVs are highly diverse and are divided into multiple genogroups based on structural protein (VP1) sequences. SaVs detected from pigs belong to eight genogroups (GIII, GV, GVI, GVII, GVIII, GIX, GX, and GXI), but little is known about the SaV genogroup distribution in the Japanese pig population. In the present study, 26 nearly complete genome (>6000 nucleotide: nt) and three partial sequences (2429nt, 4364nt, and 4419nt in length, including the entire VP1 coding region) of SaV were obtained from one diarrheic and 15 non-diarrheic porcine feces in Japan via a metagenomics approach. Phylogenetic analysis of the complete VP1 amino acid sequence (aa) revealed that 29 porcine SaVs were classified into seven genogroups; GIII (11 strains), GV (1 strain), GVI (3 strains), GVII (6 strains), GVIII (1 strain), GX (3 strains), and GXI (4 strains). This manuscript presents the first nearly complete genome sequences of GX and GXI, and demonstrates novel intergenogroup recombination events.

Norovirus GII.Pe Genotype: Tracking a Foodborne Outbreak on a Cruise Ship Through Molecular Epidemiology, Brazil, 2014

Norovirus (NoV) is recognized as the most common cause of foodborne outbreaks. In 2014, an outbreak of acute gastroenteritis occurred on a cruise ship in Brazil, and NoV became the suspected etiology. Here we present the molecular identification of the NoV strains and the use of sequence analysis to determine modes of virus transmission. Food (cream cheese, tuna salad, grilled fish, orange mousse, and vegetables soup) and clinical samples were analyzed by ELISA, conventional RT-PCR, qRT-PCR, and sequencing. Genogroup GII NoV was identified by ELISA and conventional RT-PCR in fecal samples from 5 of 12 patients tested (41.7%), and in the orange mousse food sample by conventional RT-PCR and qRT-PCR. Two fecal GII NoV samples and the orange mousse GII NoV sample were successfully genotyped as GII.Pe (ORF 1), revealed 98.0-98.8% identities among them, and shared phylogenetically distinct cluster. Establishing the source of a NoV outbreak can be a challenging task. In this report, the molecular analysis of the partial RdRp NoV gene provided a powerful tool for genotyping (GII.Pe) and tracking of outbreak-related samples. In addition, the same fast and simple extraction methods applied to clinical samples could be successfully used for complex food matrices, and have the potential to be introduced in routine laboratories for screening foods for presence of NoV.

Human and Animal Viruses in Food (Including Taxonomy of Enteric Viruses)

In recent years, there has been an increase in the incidence of foodborne diseases worldwide, with viruses now being recognized as a major cause of these illnesses. The most common viruses implicated in foodborne disease are enteric viruses, which are found in the human gastrointestinal tract, excreted in human feces and transmitted by the fecal-oral route. Many different viruses are found in the gastrointestinal tract but not all are recognized as foodborne pathogens. The diseases caused by enteric viruses fall into three main types: gastroenteritis, enterically transmitted hepatitis, and illnesses that can affect other parts of the body such as the eye, the respiratory system and the central nervous system leading to conjunctivitis, poliomyelitis, meningitis and encephalitis. Viral pathogens excreted in human feces include noroviruses, sapoviruses, enteroviruses, adenoviruses, hepatitis A virus (HAV), hepatitis E virus (HEV), rotaviruses, and astroviruses. Most of these viruses have been associated with foodborne disease outbreaks. Noroviruses and HAV are commonly identified as foodborne causes of gastroenteritis and acute hepatitis, respectively.

Shellfish-Associated Enteric Virus Illness: Virus Localization, Disease Outbreaks and Prevention

Numerous outbreaks of shellfish-borne enteric virus illness have been reported worldwide. Most notable among the outbreaks are those caused by NoV and HAV. Lessons learned from outbreak investigations indicate that most outbreaks are preventable. Anthropogenic sources of contamination will continue to invade shellfish growing waters. Shellfish, by their very nature, will continue to bioconcentrate these contaminants, including enteric viruses. There is no quick fix for enteric virus contamination of shellfish; however, vigilance on behalf of the industry, regulatory agencies, and the consumer could substantially reduce the incidence of illness. Enhanced monitoring in all areas of shellfish production, harvesting, distribution, and processing would help to reduce viral illnesses. Pollution abatement and improved hygienic practices on behalf of the industry and consumers are needed. Improved analytical techniques for the detection of enteric viruses in shellfish will lead to enhanced shellfish safety and better protection for the consumer and the industry. Better reporting and epidemiological follow-up of outbreaks are keys to reducing the transmission of foodborne viral infections. It is anticipated that recent advances in analytical techniques, particularly for NoV, will lead to better monitoring capabilities for food and water and a reduction in the incidence of enteric virus illness among shellfish consumers.

The application of phage-based faecal pollution markers to predict the concentration of adenoviruses in mussels (Mytilus edulis) and their overlying waters

AIM

This study set out to determine whether phage-based indicators may provide a 'low-tech' alternative to existing approaches that might help maintain the microbial safety of shellfish and their overlying waters.

METHODS AND RESULTS

Mussels and their overlying waters were collected biweekly from an estuary in southeast England over a 2-year period (May 2013-April 2015) (n = 48). Levels of bacterial indicators were determined using membrane filtration and most probable number methods and those of bacteriophages were determined by direct plaque assay. The detection of adenovirus was determined using real-time polymerase chain reaction. The results revealed that somatic coliphages demonstrated the most significant correlations with AdV F and G in mussels (ρ = 0·55) and overlying waters (ρ = 0·66), followed by GB124 phages (ρ = 0·43) while Escherichia coli showed no correlation with AdV F and G in mussels.

CONCLUSION

This study demonstrates that the use of somatic coliphages and GB124 phages may provide a better indication of the risk of adenovirus contamination of mussels and their overlying waters than existing bacterial indicators.

SIGNIFICANCE AND IMPACT OF THE STUDY

Phage-based detection may be particularly advantageous in low-resource settings where viral infectious disease presents a significant burden to human health.

Prevalence and Genetic Diversity of Human Sapoviruses in Shellfish from Commercial Production Areas in Galicia, Spain

The prevalence of human forms of Sapovirus, an emerging pathogen of human gastroenteritis, was investigated in an 18-month survey from class B mollusc-harvesting areas in two Galician rias (northwest Spain). The detection and quantification of Sapovirus was performed by reverse transcription-real-time PCR, according to the recently developed standard method ISO/TS 15216-1:2013, and genotyping by reverse transcription-nested PCR. The bivalve species studied were wild and cultured mussels (Mytilus galloprovincialis), clams (Venerupis philippinarum and Venerupis decussata), and cockles (Cerastoderma edule). Sapovirus was detected in 30 out of 168 samples (17.9%), with cockles being the species with the highest prevalence of positives (28.1%), followed by clams (22.6%), wild mussels (14.3%), and cultured mussels (12.9%). The estuary in the south of the region demonstrated a higher percentage of positive samples (21.8%) than the one in the north (14.4%). Viral contamination levels for the positive samples ranged between 1.9 × 10(3) and 1.4 × 10(5) RNA copies/g of digestive tissue. Thirteen Sapovirus sequences could be obtained based on partial capsid gene sequence and were classified into four genotypes: GI.1 (2 samples), GI.2 (8 samples), GIV.1 (2 samples), and GV.1 (1 sample).

Detection and Genetic Analysis of Noroviruses and Sapoviruses in Sea Snail

An outbreak of acute gastroenteritis occurred at a restaurant in Yokohama in December 2011. Because many of the customers had consumed raw sea snail, sea snail was suspected to be the source of this outbreak. To determine whether sea snail contains Norovirus (NoV) or Sapovirus (SaV), we analyzed 27 sea snail samples collected over 5 months (May, June, August, October, and December 2012) and 59.3% were positive for NoV and/or SaV. The levels of NoV ranged from 1.5 × 10(3) to 1.5 × 10(5) copies/g tissue, and those of SaV from 1.5 × 10(2) to 1.3 × 10(3) copies/g tissue. The highest levels were observed in sea snails collected in December. A phylogenetic analysis of the NoVs showed that the viral strains were NoV genotypes GI.4, GI.6, GII.4, GII.12, GII.13, and GII.14, and the SaV strains were genotypes GI.2 and GI.3. The NoV GII.4 Sydney 2012 variants were only detected in December. This variant was a major source of gastroenteritis in Japan in the winter of 2012/2013. In contrast, the NoV GII.4 strains detected in May and June 2012 were not the Sydney 2012 variant. This study demonstrates that sea snail contains multiple genogroups and genotypes of NoV and SaV strains. We conclude that the sea snail presents a risk of gastroenteritis when consumed raw.

Quantification and molecular characterisation of human sapoviruses in water sources impacted by highly polluted discharged wastewater in South Africa

Sapoviruses (SaVs) were detected and quantified in 8/10 water samples collected from wastewater treatment works (WWTWs) and water sources impacted by these WWTWs in Limpopo Province, South Africa. The median SaV concentration was 2.45 × 10⁶ copies/L and SaV genotypes I.2 and IV were characterised. This study provides new data on the high concentrations of clinically relevant SaVs in rivers and dams impacted by poor-performing WWTWs.

The impact of calicivirus mixed infection in an oyster-associated outbreak during a food festival

BACKGROUND

Despite calicivirus food-borne outbreaks posing major public health concern worldwide, little information is at present available about the impact of caliciviruses mixed infection in an oyster-associated outbreak in China.

OBJECTIVES

To investigate the clinical and epidemiologic characteristics of an oyster-associated calicivirus outbreak initiated by a food festival in Shanghai, China, in April 2014.

STUDY DESIGN

Molecular epidemiological studies based on nucleotide sequencing and phylogenetic analysis of calicivirus strains from patients.

RESULTS

A total of 65 of the 78 (83%) cases from this outbreak were associated with raw oyster consumption. Forty-six calicivirus strains were identified from 25 stool specimens with norovirus (NoV) GII.4 Sydney_2012, GII.13, GI.2, GI.5 and sapovirus (SaV) GI.2 being predominant genotypes and with a prevalence of triple-, double- and single-infection being 20%, 48% and 28%, respectively. Meanwhile, 13 putative NoV recombinants were indicated by the phylogenetic inconsistency between capsid and polymerase genotype, mainly including GII.Pe/GII.4 Sydney_2012. Molecular epidemiological investigation showed possible multiple route transmission in the field. The clinical and epidemiologic characteristics of the mixed point-source calicivirus outbreak also conformed to Kaplan's criteria.

CONCLUSIONS

This is the first reported oyster-associated calicivirus outbreak with a high prevalence of mixed infection during a food festival described in China. Our investigation underscores the importance of early surveillance and comprehensive etiologic identification of mixed point-source outbreaks and the need for reliable standards of monitoring oysters to prevent and control calicivirus food-borne outbreaks in China.

Comprehensive review of human sapoviruses

Sapoviruses cause acute gastroenteritis in humans and animals. They belong to the genus Sapovirus within the family Caliciviridae. They infect and cause disease in humans of all ages, in both sporadic cases and outbreaks. The clinical symptoms of sapovirus gastroenteritis are indistinguishable from those caused by noroviruses, so laboratory diagnosis is essential to identify the pathogen. Sapoviruses are highly diverse genetically and antigenically. Currently, reverse transcription-PCR (RT-PCR) assays are widely used for sapovirus detection from clinical specimens due to their high sensitivity and broad reactivity as well as the lack of sensitive assays for antigen detection or cell culture systems for the detection of infectious viruses. Sapoviruses were first discovered in 1976 by electron microscopy in diarrheic samples of humans. To date, sapoviruses have also been detected from several animals: pigs, mink, dogs, sea lions, and bats. In this review, we focus on genomic and antigenic features, molecular typing/classification, detection methods, and clinical and epidemiological profiles of human sapoviruses.

Detection of multiple human sapoviruses from imported frozen individual clams

Sapovirus (SaV), a member of the family Caliciviridae, is an important acute gastroenteritis pathogen in humans. Consumption of raw or inadequately cooked clams is one transmission route of human SaV. Sixty individual clams (Ruditapes philippinarum) were from market and tested for human SaVs using two nested reverse transcription-polymerase chain reaction (RT-PCR) assays, one of which was recently developed and effectively detected human SaV from environmental water samples. The nested RT-PCR effective for water samples showed a higher detection rate (68.3 %, 41 of 60 clams) than the other nested RT-PCR (43.3 %, 26 of 60 clams). Based on the sequence analysis of the partial capsid region, SaV strains detected in this study were classified into nine genotypes: GI.1, GI.3, GI.5, GI.6, GI.7, GII.3, GII.4, GIV.1, and GV.1. We demonstrated for the first time the presence of multiple genogroups and/or genotypes of SaV strains in the individual clams. Using a more sensitive assay such as we described to test individual clam samples will help to identify the source of a SaV-gastroenteritis outbreak.

Novel monoclonal antibodies broadly reactive to human recombinant sapovirus-like particles

Sapovirus (SaV), a member of the family Caliciviridae, is an important cause of acute epidemic gastroenteritis in humans. Human SaV is genetically and antigenically diverse and can be classified into four genogroups (GI, GII, GIV, and GV) and 16 genotypes (7 GI [GI.1-7], 7 GII, [GII.1-7], 1 GIV and 1 GV), based on capsid sequence similarities. Monoclonal antibodies (MAbs) are powerful tools for examining viruses and proteins. PAI myeloma cells were fused with spleen cells from mice immunized with a single type of recombinant human SaV virus-like particles (VLPs) (GI.1, GI.5, GI.6, GII.3, GIV, or GV). Sixty-five hybrid clones producing MAbs were obtained. Twenty-four MAbs were characterized by ELISA, according to their cross-reactivity to each VLP (GI.1, GI.5, GI.6, GII.2, GII.3, GII.4, GII.7, GIV, and GV). The MAbs were classified by this method into: (i) MAbs broadly cross-reactive to all GI, GII, GIV and GV strains; (ii) those reactive in a genogroup-specific; and (iii) those reactive in a genotype-specific manner. Further analysis of three broadly cross-reactive MAbs with a competitive ELISA demonstrated that at least two different common epitopes are located on the capsid protein of human SaVs in the four genogroups. The MAbs generated and characterized in this study will be useful tools for further study of the antigenic and structural topography of the human SaV virion and for developing new diagnostic assays for human SaV.

Application of a competitive internal amplification control for the detection of sapoviruses in wastewater

In this study, a competitive internal amplification control (IAC) was constructed for application in the real-time reverse transcription-polymerase chain reaction detection of sapoviruses (SaVs). A SaV RNA standard was also created for quantification of the virus. The IAC was included in the screening of environmental samples for SaVs. From August 2010 to December 2011, 51 wastewater samples were collected from five provinces in South Africa. SaVs were found in 72.5 % (37/51) of samples, including four samples where detection was initially inhibited. SaV concentrations ranged from 4.24 × 10(3) to 1.31 × 10(6) copies/ml. The IAC successfully identified samples which contained inhibitors and inclusion of an IAC is necessary to ensure the prevalence of SaVs is accurately determined. SaVs are present at high concentrations in wastewater in several provinces of South Africa. This widespread occurrence indicates that SaV circulation in the South African population may be underestimated.

Shellfish-borne viral outbreaks: a systematic review

Investigations of disease outbreaks linked to shellfish consumption have been reported in the scientific literature; however, only few countries systematically collate and report such data through a disease surveillance system. We conducted a systematic review to investigate shellfish-borne viral outbreaks and to explore their distribution in different countries, and to determine if different types of shellfish and viruses are implicated. Six databases (Medline, Embase, Scopus, PubMed, Eurosurveillance Journal and Spingerlink electronic Journal) and a global electronic reporting system (ProMED) were searched from 1980 to July 2012. About 359 shellfish-borne viral outbreaks, alongside with nine ProMED reports, involving shellfish consumption, were identified. The majority of the reported outbreaks were located in East Asia, followed by Europe, America, Oceania, Australia and Africa. More than half of the outbreaks (63.6 %) were reported from Japan. The most common viral pathogens involved were norovirus (83.7 %) and hepatitis A virus (12.8 %). The most frequent type of consumed shellfish which was involved in outbreaks was oysters (58.4 %). Outbreaks following shellfish consumption were often attributed to water contamination by sewage and/or undercooking. Differences in reporting of outbreaks were seen between the scientific literature and ProMED. Consumption of contaminated shellfish represents a risk to public health in both developed and developing countries, but impact will be disproportionate and likely to compound existing health disparities.

High pressure processing and its application to the challenge of virus-contaminated foods

High pressure processing (HPP) is an increasingly popular non-thermal food processing technology. Study of HPP's potential to inactivate foodborne viruses has defined general pressure levels required to inactivate hepatitis A virus, norovirus surrogates, and human norovirus itself within foods such as shellfish and produce. The sensitivity of a number of different picornaviruses to HPP is variable. Experiments suggest that HPP inactivates viruses via denaturation of capsid proteins which render the virus incapable of binding to its receptor on the surface of its host cell. Beyond the primary consideration of treatment pressure level, the effects of extending treatment times, temperature of initial pressure application, and matrix composition have been identified as critical parameters for designing HPP inactivation strategies. Research described here can serve as a preliminary guide to whether a current commercial process could be effective against HuNoV or HAV.

A confirmation of sapovirus re-infection gastroenteritis cases with different genogroups and genetic shifts in the evolving sapovirus genotypes, 2002-2011

Sapovirus (SaV) is an important pathogen that causes acute gastroenteritis in humans. Human SaV is highly diverse genetically and is classified into multiple genogroups and genotypes. At present, there is no clear evidence for gastroenteritis cases caused by re-infection with SaV. We found that two individuals were sequentially infected with SaVs of two different genogroups and had gastroenteritis after each infection, although in one of the subsequent cases, both SaV and norovirus were detected. We also found a genetic shift in SaVs from gastroenteritis outpatients in the same geographical location. Our results suggest that protective immunity may be at least genogroup-specific for SaV.

Presence of hepatitis E RNA in mussels used as bio-monitors of viral marine pollution

Mussels (Mytilus galloprovincialis), collected from a harvesting area approved by European Community Regulation, were transplanted to four polluted sites located in the Northwestern Mediterranean area (Tuscany). They were used as bio-monitors to test the quality of the marine water pollution. At different times after the transplantation, mussels were withdrawn and tested for presence of phages and enteric viruses by molecular tests. 52.4% of the transplanted mussel samples were positive for at least one enteric virus. Hepatitis A virus (HAV) was identified in each site (17/37; 45.9%). Three samples were positive for hepatitis E virus (HEV) (8.1%) and two (5.4%) for norovirus (NoV) genogroup I. Coliphages and RYC 2056 phages were detected in all sites, while HSP 40 phages were detected in three sites. Results demonstrate the ability of transplanted mussels in accumulating and retaining different species of enteric microorganisms. Their utility as bio-monitor organisms enables testing for viral marine pollution.

Norovirus Monitoring in Bivalve Molluscs Harvested and Commercialized in Southern Italy

Norovirus (NoV) is the main cause of human nonbacterial gastroenteritis throughout the world. NoVs are classified into five genogroups: GI, GII, GIII, GIV, and GV. NoVs from GI and GII are the most commonly reported NoVs associated with human infections, and raw or undercooked shellfish have been identified as the main potential infection vehicle. European Commission Regulation 2073/2005 defines only bacteriological parameters for use as safety criteria for shellfish because reference methods for detection of viruses are lacking. From July 2007 to April 2010, 163 shellfish samples were collected in southern Italy from harvesting areas, authorized or nonauthorized retailers, and a restaurant after an outbreak of human gastroenteritis. The shellfish were analyzed for the presence of NoVs from GI and GII using the one-step real-time reverse transcription PCR protocol. A total of 94 shellfish samples (57.7%) were positive for the presence of NoV, and GII was the most frequently identified genogroup.

Transmission of viruses through shellfish: when specific ligands come into play

Shellfish are known as vectors for human pathogens and despite regulation based on enteric bacteria they are still implicated in viral outbreaks. Among shellfish, oysters are the most common vector of contamination, and the pathogens most frequently involved in these outbreaks are noroviruses, responsible for acute gastroenteritis in humans. Analysis of shellfish-related outbreak data worldwide show an unexpected high proportion of NoV GI strains. Recent studies performed in vitro, in vivo and in the environment indicate that oysters are not just passive filters, but can selectively accumulate norovirus strains based on viral carbohydrate ligands shared with humans. These observations contribute to explain the GI bias observed in shellfish-related outbreaks compared to other outbreaks.

Prevalence and diversity of norovirus genogroups I and II in Hong Kong marine waters and detection by real-time PCR

Marine waters from six sites around Hong Kong with varying levels of sewage pollution were examined for noroviruses (NoVs) by PCR cloning and sequencing of a highly-variable N-terminal region of the VP1 capsid gene, at the ORF1-ORF2 junction of NoV. Phylogenetic analysis of genogroups GI- and GII-specific PCR clones obtained from different marine sites indicated that human NoV GI.1 and GII.4 strains are the most prevalent genotypes circulating in Hong Kong waters. GI- and GII-specific TaqMan-based real-time PCR assays targeting the ORF1-ORF2 junction of NoVs were used to quantify NoV particles in marine water samples in parallel with total Escherichia coli counts which were enumerated on TBX medium. No correlation of any significance between NoV and E. coli counts was observed which highlighted the inadequacy in using E. coli as a fecal indicator to predict the level of NoVs in marine waters to protect public health.

Human sapovirus classification based on complete capsid nucleotide sequences

The genetically diverse sapoviruses (SaVs) are a significant cause of acute human gastroenteritis. Human SaV surveillance is becoming more critical, and a better understanding of the diversity and distribution of the viral genotypes is needed. In this study, we analyzed 106 complete human SaV capsid nucleotide sequences to provide a better understanding of their diversity. Based on those results, we propose a novel standardized classification scheme that meets the requirements of the International Calicivirus Scientific Committee. We believe the classification scheme and strains described here will be of value for the molecular characterization and classification of newly detected SaV genotypes and for comparing data worldwide.

First description of gastroenteritis viruses in Lebanese children: a pilot study

Human enteric viruses are important causes of acute gastroenteritis in infants and children. The role of rotaviruses, adenoviruses, human caliciviruses and astroviruses in the development of severe acute gastroenteritis requiring hospitalization of infants and young children in North Lebanon was investigated. Stool specimens collected between April and May 2010 from 79 Lebanese infants and children hospitalized for severe acute gastroenteritis, were screened for enteric viruses by immunoassays and internally controlled multiplex PCR assay. Out of 79 stool samples, 38 (48%) were positive for rotavirus, and 5 (6%) were positive for norovirus genogroup II. Enteric adenoviruses, sapoviruses and human astroviruses were not detected. Children with severe rotavirus gastroenteritis were younger than those with severe norovirus gastroenteritis. These results highlight the importance of rotavirus and norovirus as causes of severe gastroenteritis in Lebanese children, and the need to incorporate routine screening tests for norovirus infection in clinical settings.

Genotype distribution of human sapoviruses in wastewater in Japan

Human sapovirus sequences were identified in 12 (100%) influent and 7 (58%) effluent wastewater samples collected once a month for a year. The strains were characterized based on their partial capsid gene sequences and classified into 10 genotypes, demonstrating that genetically diverse sapovirus strains infect humans in the study area.

Strain-dependent norovirus bioaccumulation in oysters

Noroviruses (NoVs) are the main agents of gastroenteritis in humans and the primary pathogens of shellfish-related outbreaks. Some NoV strains bind to shellfish tissues by using carbohydrate structures similar to their human ligands, leading to the hypothesis that such ligands may influence bioaccumulation. This study compares the bioaccumulation efficiencies and tissue distributions in oysters (Crassostrea gigas) of three strains from the two principal human norovirus genogroups. Clear differences between strains were observed. The GI.1 strain was the most efficiently concentrated strain. Bioaccumulation specifically occurred in digestive tissues in a dose-dependent manner, and its efficiency paralleled ligand expression, which was highest during the cold months. In comparison, the GII.4 strain was very poorly bioaccumulated and was recovered in almost all tissues without seasonal influence. The GII.3 strain presented an intermediate behavior, without seasonal effect and with less bioaccumulation efficiency than that of the GI.1 strain during the cold months. In addition, the GII.3 strain was transiently concentrated in gills and mantle before being almost specifically accumulated in digestive tissues. Carbohydrate ligand specificities of the strains at least partly explain the strain-dependent bioaccumulation characteristics. In particular, binding to the digestive-tube-specific ligand should contribute to bioaccumulation, whereas we hypothesize that binding to the sialic acid-containing ligand present in all tissues would contribute to retain virus particles in the gills or mantle and lead to rapid destruction.

Norovirus as a foodborne disease hazard

Norovirus (NoV) is the most common cause of infectious gastroenteritis in the world. Gastroenteritis caused by bacterial and parasitic pathogens is commonly linked to food sources, but the link between NoV and contaminated foods has been more difficult to establish. Even when epidemiological information indicates that an outbreak originated with food, the presence of NoV in the suspect product may not be confirmed. If food is found to contain a common strain of NoV that circulates widely in the community, it is not possible to use strain typing to link the contamination to patient cases. Although food is certainly implicated in NoV spread, there are additional person-to-person and fomite transmission routes that have been shown to be important. NoV has an extremely low infectious dose, is stable in the environment, and resists disinfection. Cell culture methods are not available, so viability cannot be determined. Finally, many NoV outbreaks originate with when an infected food handler contaminates ready-to-eat food, which can be interpreted as foodborne or person-to-person transmission. This review will discuss both the physical characteristics of NoVs and the available epidemiological information with particular reference to the role of foods in NoV transmission.