A Comprehensive Review for the Surveillance of Human Pathogenic Microorganisms in Shellfish

Bivalve molluscan shellfish have been consumed for centuries. Being filter feeders, they may bioaccumulate some microorganisms present in coastal water, either naturally or through the discharge of human or animal sewage. Despite regulations set up to avoid microbiological contamination in shellfish, human outbreaks still occur. After providing an overview showing their implication in disease, this review aims to highlight the diversity of the bacteria or enteric viruses detected in shellfish species, including emerging pathogens. After a critical discussion of the available methods and their limitations, we address the interest of technological developments using genomics to anticipate the emergence of pathogens. In the coming years, further research needs to be performed and methods need to be developed in order to design the future of surveillance and to help risk assessment studies, with the ultimate objective of protecting consumers and enhancing the microbial safety of bivalve molluscan shellfish as a healthy food.

Porcine Epidemic Diarrhea Virus, Surrogate for Coronavirus Decay Measurement in French Coastal Waters and Contribution to Coronavirus Risk Evaluation

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in infected patients mainly displays pulmonary and oronasal tropism; however, the presence of the virus has also been demonstrated in the stools of patients and consequently in wastewater treatment plant effluents, raising the question of the potential risk of environmental contamination (such as seawater contamination) through inadequately treated wastewater spillover into surface or coastal waters even if the environmental detection of viral RNA alone does not substantiate risk of infection. Therefore, here, we decided to experimentally evaluate the persistence of the porcine epidemic diarrhea virus (PEDv), considered as a coronavirus representative model, in the coastal environment of France. Coastal seawater was collected, sterile-filtered, and inoculated with PEDv before incubation for 0 to 4 weeks at four temperatures representative of those measured along the French coasts throughout the year (4, 8, 15, and 24°C). The decay rate of PEDv was determined using mathematical modeling and was used to determine the half-life of the virus along the French coast in accordance with temperatures from 2000 to 2021. We experimentally observed an inverse correlation between seawater temperature and the persistence of infectious viruses in seawater and confirm that the risk of transmission of infectious viruses from contaminated stool in wastewater to seawater during recreational practices is very limited. The present work represents a good model to assess the persistence of coronaviruses in coastal environments and contributes to risk evaluation, not only for SARS-CoV-2 persistence, but also for other coronaviruses, specifically enteric coronaviruses from livestock. IMPORTANCE The present work addresses the question of the persistence of coronavirus in marine environments because SARS-CoV-2 is regularly detected in wastewater treatment plants, and the coastal environment, subjected to increasing anthropogenic pressure and the final receiver of surface waters and sometimes insufficiently depurated wastewater, is particularly at risk. The problem also arises in the possibility of soil contamination by CoV from animals, especially livestock, during manure application, where, by soil impregnation and runoff, these viruses can end up in seawater. Our findings are of interest to researchers and authorities seeking to monitor coronaviruses in the environment, either in tourist areas or in regions of the world where centralized systems for wastewater treatment are not implemented, and more broadly, to the scientific community involved in "One Health" approaches.

Species-Specific N-Glycomes and Methylation Patterns of Oysters Crassostrea gigas and Ostrea edulis and Their Possible Consequences for the Norovirus-HBGA Interaction

Noroviruses, the major cause of acute viral gastroenteritis, are known to bind to histo-blood group antigens (HBGAs), including ABH groups and Lewis-type epitopes, which decorate the surface of erythrocytes and epithelial cells of their host tissues. The biosynthesis of these antigens is controlled by several glycosyltransferases, the distribution and expression of which varies between tissues and individuals. The use of HBGAs as ligands by viruses is not limited to humans, as many animal species, including oysters, which synthesize similar glycan epitopes that act as a gateway for viruses, become vectors for viral infection in humans. Here, we show that different oyster species synthesize a wide range of N-glycans that share histo-blood A-antigens but differ in the expression of other terminal antigens and in their modification by O-methyl groups. In particular, we show that the N-glycans isolated from Crassostrea gigas and Ostrea edulis exhibit exquisite methylation patterns in their terminal N-acetylgalactosamine and fucose residues in terms of position and number, adding another layer of complexity to the post-translational glycosylation modifications of glycoproteins. Furthermore, modeling of the interactions between norovirus capsid proteins and carbohydrate ligands strongly suggests that methylation has the potential to fine-tune the recognition events of oysters by virus particles.

Human Sapovirus Replication in Human Intestinal Enteroids

Human sapoviruses (HuSaVs), like human noroviruses (HuNoV), belong to the Caliciviridae family and cause acute gastroenteritis in humans. Since their discovery in 1976, numerous attempts to grow HuSaVs in vitro were unsuccessful until 2020, when these viruses were reported to replicate in a duodenal cancer cell-derived line. Physiological cellular models allowing viral replication are essential to investigate HuSaV biology and replication mechanisms such as genetic susceptibility, restriction factors, and immune responses to infection. In this study, we demonstrate replication of two HuSaV strains in human intestinal enteroids (HIEs) known to support the replication of HuNoV and other human enteric viruses. HuSaVs replicated in differentiated HIEs originating from jejunum, duodenum and ileum, but not from the colon, and bile acids were required. Between 2h and 3 to 6 days postinfection, viral RNA levels increased up from 0.5 to 1.8 log10-fold. Importantly, HuSaVs were able to replicate in HIEs independent of their secretor status and histo-blood group antigen expression. The HIE model supports HuSaV replication and allows a better understanding of host-pathogen mechanisms such as cellular tropism and mechanisms of viral replication. IMPORTANCE Human sapoviruses (HuSaVs) are a frequent but overlooked cause of acute gastroenteritis, especially in children. Little is known about this pathogen, whose successful in vitro cultivation was reported only recently, in a cancer cell-derived line. Here, we assessed the replication of HuSaV in human intestinal enteroids (HIEs), which are nontransformed cultures originally derived from human intestinal stem cells that can be grown in vitro and are known to allow the replication of other enteric viruses. Successful infection of HIEs with two strains belonging to different genotypes of the virus allowed discovery that the tropism of these HuSaVs is restricted to the small intestine, does not occur in the colon, and replication requires bile acid but is independent of the expression of histo-blood group antigens. Thus, HIEs represent a physiologically relevant model to further investigate HuSaV biology and a suitable platform for the future development of vaccines and antivirals.

Looking into sewage: how far can metagenomics help to detect human enteric viruses?

The impact of human sewage on environmental and food contamination constitutes an important safety issue. Indeed, human sewage reflects the microbiome of the local population, and a variety of human viruses can be detected in wastewater samples. Being able to describe the diversity of viruses present in sewage will provide information on the health of the surrounding population health and will help to prevent further transmission. Metagenomic developments, allowing the description of all the different genomes present in a sample, are very promising tools for virome analysis. However, looking for human enteric viruses with short RNA genomes which are present at low concentrations is challenging. In this study we demonstrate the benefits of performing technical replicates to improve viral identification by increasing contig length, and the set-up of quality criteria to increase confidence in results. Our approach was able to effectively identify some virus sequences and successfully describe the viral diversity. The method yielded full genomes either for norovirus, enterovirus and rotavirus, even if, for these segmented genomes, combining genes remain a difficult issue. Developing reliable viromic methods is important as wastewater sample analysis provides an important tool to prevent further virus transmission by raising alerts in case of viral outbreaks or emergence.

Development of passive samplers for the detection of SARS-CoV-2 in sewage and seawater: Application for the monitoring of sewage

Recent studies have shown that passive sampling is a promising tool for SARS-CoV-2 detection for wastewater-based epidemiology (WBE) application. We have previously developed passive sampling of viruses using polymer membranes in seawater. Even though SARS-CoV-2 was not detected yet in seawater, passive sampling could be optimized for future application in coastal areas close to wastewater treatment plant (WWTP). The aim of this study was to optimize passive sampling of SARS-CoV-2 in sewage and seawater by selecting a suitable membrane, to determine whether the quantities of virus increase over time, and then to determine if passive sampling and traditional sampling are correlated when conducted in a wastewater treatment plant. Nylon and Zetapor allowed the detection of heat inactivated SARS-CoV-2 and of the Porcine Epidemic Diarrhea Virus (PEDV), a coronavirus surrogate, in wastewater and seawater spiked with these 2 viruses, showing an increase in detection between 4 h and 24 h of immersion and significantly higher recoveries of both viruses with nylon in seawater (15%) compared to wastewater (4%). On wastewater samples, both membranes detected the virus, the recovery rate was of about 3% for freshly collected samples, and no significant difference was found between SARS-CoV-2 genome concentration on Zetapor and that in water. In sewage spiked seawater, similar concentrations of genome were found on both membranes, with a mean recovery rate of 16% and 11% respectively for nylon and Zetapor. A 3-weeks monitoring with passive sampler allowed the detection of viruses in the influent of a WWTP with a frequency of 100% and 76% for SARS-CoV-2 and norovirus GII respectively. Passive and traditional sampling gave the same evolution of the SARS-CoV-2 concentration over time. All these results confirmed the interest of passive sampling for virus detection and its potential application for monitoring in the wastewater system for targeted public health actions.

Use of Human Intestinal Enteroids to Evaluate Persistence of Infectious Human Norovirus in Seawater

Little data on the persistence of human norovirus infectivity are available to predict its transmissibility. Using human intestinal enteroids, we demonstrate that 2 human norovirus strains can remain infectious for several weeks in seawater. Such experiments can improve understanding of factors associated with norovirus survival in coastal waters and shellfish.

SARS-CoV-2 Whole-Genome Sequencing Using Oxford Nanopore Technology for Variant Monitoring in Wastewaters

Since the beginning of the Coronavirus Disease-19 (COVID-19) pandemic, multiple Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) mutations have been reported and led to the emergence of variants of concern (VOC) with increased transmissibility, virulence or immune escape. In parallel, the observation of viral fecal shedding led to the quantification of SARS-CoV-2 genomes in wastewater, providing information about the dynamics of SARS-CoV-2 infections within a population including symptomatic and asymptomatic individuals. Here, we aimed to adapt a sequencing technique initially designed for clinical samples to apply it to the challenging and mixed wastewater matrix, and hence identify the circulation of VOC at the community level. Composite raw sewage sampled over 24 h in two wastewater-treatment plants (WWTPs) from a city in western France were collected weekly and SARS-CoV-2 quantified by RT-PCR. Samples collected between October 2020 and May 2021 were submitted to whole-genome sequencing (WGS) using the primers and protocol published by the ARTIC Network and a MinION Mk1C sequencer (Oxford Nanopore Technologies, Oxford, United Kingdom). The protocol was adapted to allow near-full genome coverage from sewage samples, starting from ∼5% to reach ∼90% at depth 30. This enabled us to detect multiple single-nucleotide variant (SNV) and assess the circulation of the SARS-CoV-2 VOC Alpha, Beta, Gamma, and Delta. Retrospective analysis of sewage samples shed light on the emergence of the Alpha VOC with detection of first co-occurring signature mutations in mid-November 2020 to reach predominance of this variant in early February 2021. In parallel, a mutation-specific qRT-PCR assay confirmed the spread of the Alpha VOC but detected it later than WGS. Altogether, these data show that SARS-CoV-2 sequencing in sewage can be used for early detection of an emerging VOC in a population and confirm its ability to track shifts in variant predominance.

Human and Animal RNA Virus Diversity Detected by Metagenomics in Cameroonian Clams

Many recent pandemics have been recognized as zoonotic viral diseases. While their origins remain frequently unknown, environmental contamination may play an important role in emergence. Thus, being able to describe the viral diversity in environmental samples contributes to understand the key issues in zoonotic transmission. This work describes the use of a metagenomic approach to assess the diversity of eukaryotic RNA viruses in river clams and identify sequences from human or potentially zoonotic viruses. Clam samples collected over 2years were first screened for the presence of norovirus to verify human contamination. Selected samples were analyzed using metagenomics, including a capture of sequences from viral families infecting vertebrates (VirCapSeq-VERT) before Illumina NovaSeq sequencing. The bioinformatics analysis included pooling of data from triplicates, quality filtering, elimination of bacterial and host sequences, and a deduplication step before de novo assembly. After taxonomic assignment, the viral fraction represented 0.8–15% of reads with most sequences (68–87%) remaining un-assigned. Yet, several mammalian RNA viruses were identified. Contigs identified as belonging to the Astroviridae were the most abundant, with some nearly complete genomes of bastrovirus identified. Picobirnaviridae sequences were related to strains infecting bats, and few others to strains infecting humans or other hosts. Hepeviridae sequences were mostly related to strains detected in sponge samples but also strains from swine samples. For Caliciviridae and Picornaviridae, most of identified sequences were related to strains infecting bats, with few sequences close to human norovirus, picornavirus, and genogroup V hepatitis A virus. Despite a need to improve the sensitivity of our method, this study describes a large diversity of RNA virus sequences from clam samples. To describe all viral contaminants in this type of food, and being able to identify the host infected by viral sequences detected, may help to understand some zoonotic transmission events and alert health authorities of possible emergence.

Can shellfish be used to monitor SARS-CoV-2 in the coastal environment?

The emergence and worldwide spread of SARS-CoV-2 raises new concerns and challenges regarding possible environmental contamination by this virus through spillover of human sewage, where it has been detected. The coastal environment, under increasing anthropogenic pressure, is subjected to contamination by a large number of human viruses from sewage, most of them being non-enveloped viruses like norovirus. When reaching coastal waters, they can be bio-accumulated by filter-feeding shellfish species such as oysters. Methods to detect this viral contamination were set up for the detection of non-enveloped enteric viruses, and may need optimization to accommodate enveloped viruses like coronaviruses (CoV). Here, we aimed at assessing methods for the detection of CoV, including SARS-CoV-2, in the coastal environment and testing the possibility that SARS-CoV-2 can contaminate oysters, to monitor the contamination of French shores by SARS-CoV-2 using both seawater and shellfish. Using the porcine epidemic diarrhea virus (PEDV), a CoV, as surrogate for SARS-CoV-2, and Tulane virus, as surrogate for non-enveloped viruses such as norovirus, we assessed and selected methods to detect CoV in seawater and shellfish. Seawater-based methods showed variable and low yields for PEDV. In shellfish, the current norm for norovirus detection was applicable to CoV detection. Both PEDV and heat-inactivated SARS-CoV-2 could contaminate oysters in laboratory settings, with a lower efficiency than a calicivirus used as control. Finally, we applied our methods to seawater and shellfish samples collected from April to August 2020 in France, where we could detect the presence of human norovirus, a marker of human fecal contamination, but not SARS-CoV-2. Together, our results validate methods for the detection of CoV in the coastal environment, including the use of shellfish as sentinels of the microbial quality of their environment, and suggest that SARS-CoV-2 did not contaminate the French shores during the summer season.

Passive Samplers, a Powerful Tool to Detect Viruses and Bacteria in Marine Coastal Areas

The detection of viruses and bacteria which can pose a threat either to shellfish health or shellfish consumers remains difficult. The current detection methods rely on point sampling of water, a method that gives a snapshot of the microorganisms present at the time of sampling. In order to obtain better representativeness of the presence of these microorganisms over time, we have developed passive sampling using the adsorption capacities of polymer membranes. Our objectives here were to assess the feasibility of this methodology for field detection. Different types of membrane were deployed in coastal waters over 2 years and the microorganisms tested using qPCR were: human norovirus (NoV) genogroups (G)I and II, sapovirus, Vibrio spp. and the species Vibrio alginolyticus, V. cholerae, V. vulnificus, and V. parahaemolyticus, OsHV-1 virus, and bacterial markers of fecal contamination. NoV GII, Vibrio spp., and the AllBac general Bacteroidales marker were quantified on the three types of membrane. NoV GII and OsHV-1 viruses followed a seasonal distribution. All membranes were favorable for NoV GII detection, while Zetapor was more adapted for OsHV-1 detection. Nylon was more adapted for detection of Vibrio spp. and the AllBac marker. The quantities of NoV GII, AllBac, and Vibrio spp. recovered on membranes increased with the duration of exposure. This first application of passive sampling in seawater is particularly promising in terms of an early warning system for the prevention of contamination in oyster farming areas and to improve our knowledge on the timing and frequency of disease occurence.

Optimisation of a PMAxx™-RT-qPCR Assay and the Preceding Extraction Method to Selectively Detect Infectious Murine Norovirus Particles in Mussels

Human noroviruses are a major cause for gastroenteritis outbreaks. Filter-feeding bivalve molluscs, which accumulate noroviruses in their digestive tissues, are a typical vector for human infection. RT-qPCR, the established method for human norovirus detection in food, does not allow discrimination between infectious and non-infectious viruses and can overestimate potentially infectious viral loads. To develop a more accurate method of infectious norovirus load estimation, we combined intercalating agent propidium monoazide (PMAxx™)-pre-treatment with RT-qPCR assay using in vitro-cultivable murine norovirus. Three primer sets targeting different genome regions and diverse amplicon sizes were used to compare one-step amplification of a short genome fragment to three two-step long-range RT-qPCRs (7 kbp, 3.6 kbp and 2.3 kbp amplicons). Following initial assays performed on untreated infectious, heat-, or ultraviolet-inactivated murine noroviruses in PBS suspension, PMAxx™ RT-qPCRs were implemented to detect murine noroviruses subsequent to their extraction from mussel digestive tissues; virus extraction via anionic polymer-coated magnetic beads was compared with the proteinase K-dependent ISO norm. The long-range RT-qPCR process detecting fragments of more than 2.3 kbp allowed accurate estimation of the infectivity of UV-damaged murine noroviruses. While proteinase K extraction limited later estimation of PMAxx™ pre-treatment effects and was found to be unsuited to the assay, magnetic bead-captured murine noroviruses retained their infectivity. Genome copies of heat-inactivated murine noroviruses differed by 2.3 log₁₀ between RT-qPCR and PMAxx™-RT-qPCR analysis in bivalve molluscs, the PMAxx™ pre-treatment allowing a closer approximation of infectious titres. The combination of bead-based virus extraction and PMAxx™ RT-qPCR thus provides a more accurate model for the estimation of noroviral bivalve mollusc contamination than the conjunction of proteinase K extraction and RT-qPCR and has the potential (once validated utilising infectious human norovirus) to provide an added measure of security to food safety authorities in the hazard assessment of potential bivalve mollusc contamination.

Passive Samplers, a Powerful Tool to Detect Viruses and Bacteria in Marine Coastal Areas

The detection of viruses and bacteria which can pose a threat either to shellfish health or shellfish consumers remains difficult. The current detection methods rely on point sampling of water, a method that gives a snapshot of the microorganisms present at the time of sampling. In order to obtain better representativeness of the presence of these microorganisms over time, we have developed passive sampling using the adsorption capacities of polymer membranes. Our objectives here were to assess the feasibility of this methodology for field detection. Different types of membrane were deployed in coastal waters over 2 years and the microorganisms tested using qPCR were: human norovirus (NoV) genogroups (G)I and II, sapovirus, Vibrio spp. and the species Vibrio alginolyticus, V. cholerae, V. vulnificus, and V. parahaemolyticus, OsHV-1 virus, and bacterial markers of fecal contamination. NoV GII, Vibrio spp., and the AllBac general Bacteroidales marker were quantified on the three types of membrane. NoV GII and OsHV-1 viruses followed a seasonal distribution. All membranes were favorable for NoV GII detection, while Zetapor was more adapted for OsHV-1 detection. Nylon was more adapted for detection of Vibrio spp. and the AllBac marker. The quantities of NoV GII, AllBac, and Vibrio spp. recovered on membranes increased with the duration of exposure. This first application of passive sampling in seawater is particularly promising in terms of an early warning system for the prevention of contamination in oyster farming areas and to improve our knowledge on the timing and frequency of disease occurence.

A Targeted Metagenomics Approach to Study the Diversity of Norovirus GII in Shellfish Implicated in Outbreaks

Human noroviruses (NoV) cause epidemics of acute gastroenteritis (AGE) worldwide and can be transmitted through consumption of contaminated foods. Fresh products such as shellfish can be contaminated by human sewage during production, which results in the presence of multiple virus strains, at very low concentrations. Here, we tested a targeted metagenomics approach by deep-sequencing PCR amplicons of the capsid (VP1) and polymerase (RdRp) viral genes, on a set of artificial samples and on shellfish samples associated to AGE outbreaks, to evaluate its advantages and limitations in the identification of strains from the NoV genogroup (G) II. Using artificial samples, the method allowed the sequencing of most strains, but not all, and displayed variability between replicates especially with lower viral concentrations. Using shellfish samples, targeted metagenomics was compared to Sanger-sequencing of cloned amplicons and was able to identify a higher diversity of NoV GII and GIV strains. It allowed phylogenetic analyses of VP1 sequences and the identification, in most samples, of GII.17[P17] strains, also identified in related clinical samples. Despite several limitations, combining RdRp- and VP1-targeted metagenomics is a sensitive approach allowing the study NoV diversity in low-contaminated foods and the identification of NoV strains implicated in outbreaks.

Contamination of Clams with Human Norovirus and a Novel Hepatitis A Virus in Cameroon

Shellfish constitute an important protein source but may be contaminated by viruses from various origins. A study performed on clams collected in Cameroon showed a high prevalence of norovirus and hepatitis A virus. After sequencing, the hepatitis A virus showed similarities with the genotype V simian strains.

Novel opportunities for NGS-based one health surveillance of foodborne viruses

Foodborne viral infections rank among the top 5 causes of disease, with noroviruses and hepatitis A causing the greatest burden globally. Contamination of foods by infected food handlers or through environmental pollution are the main sources of foodborne illness, with a lesser role for consumption of products from infected animals. Viral partial genomic sequencing has been used for more than two decades to track foodborne outbreaks and whole genome or metagenomics next-generation-sequencing (NGS) are new additions to the toolbox of food microbiology laboratories. We discuss developments in the field of targeted and metagenomic NGS, with an emphasis on application in food virology, the challenges and possible solutions towards future routine application.

Metagenomic to evaluate norovirus genomic diversity in oysters: Impact on hexamer selection and targeted capture-based enrichment

Human virus transmission through food consumption has been identified since many years and the international trade increases the risk of dissemination of viral pathogens. The development of metagenomic approach holds many promises for the surveillance of viruses in food and water. This work aimed to analyze norovirus diversity and to evaluate strain-dependent accumulation patterns in three oyster types by using a metagenomic approach. Different hexamer sets to prime cDNA were evaluated before capture-based approach to enhance virus reads recovery during deep sequencing. The study includes the use of technical replicates of artificially contaminated oysters and the analysis of multiple negatives controls. Results showed a clear impact of the hexamer set used for cDNA synthesis. A set of In-house designed (I-HD) hexamers, selected to lower mollusk amplification, gave promising results in terms of viral reads abundancy. However, the best correlation between C_T values, thus concentrations, and number of reads was observed using random hexamers. Random hexamers also provided the highest numbers of reads and allowed the identification of sequence of different human enteric viruses. Regarding human norovirus, different genogroups and genotypes were identified among contigs longer than 500 bp. Two full genomes and six sequences longer than 3600 bases were obtained allowing a precise strain identification. The use of technical triplicates was found valuable to increase the chances to sequence viral strains present at low concentrations. Analyzing viral contamination in shellfish samples is quite challenging, however this work demonstrates that the recovery of full genome or long contigs, allowing clear identification of viral strains is possible.

Characterization of Norovirus and Other Human Enteric Viruses in Sewage and Stool Samples Through Next-Generation Sequencing

This study aimed to optimize a method to identify human enteric viruses in sewage and stool samples using random primed next-generation sequencing. We tested three methods, two employed virus enrichment based on the binding properties of the viral capsid using pig-mucin capture or by selecting viral RNA prior to library preparation through a capture using the SureSelect target enrichment. The third method was based on a non-specific biophysical precipitation with polyethylene glycol. Full genomes of a number of common human enteric viruses including norovirus, rotavirus, husavirus, enterovirus and astrovirus were obtained. In stool samples full norovirus genome were detected as well as partial enterovirus genome. A variety of norovirus sequences was detected in sewage samples, with genogroup II being more prevalent. Interestingly, the pig-mucin capture enhanced not only the recovery of norovirus and rotavirus but also recovery of astrovirus, sapovirus and husavirus. Documenting sewage virome using these methods provides information for molecular epidemiology and may be useful in developing strategies to prevent further spread of viruses.

Metavirome Sequencing to Evaluate Norovirus Diversity in Sewage and Related Bioaccumulated Oysters

Metagenomic sequencing is a promising method to determine the virus diversity in environmental samples such as sewage or shellfish. However, to identify the short RNA genomes of human enteric viruses among the large diversity of nucleic acids present in such complex matrices, method optimization is still needed. This work presents methodological developments focused on norovirus, a small ssRNA non-enveloped virus known as the major cause of human gastroenteritis worldwide and frequently present in human excreta and sewage. Different elution protocols were applied and Illumina MiSeq technology were used to study norovirus diversity. A double approach, agnostic deep sequencing and a capture-based approach (VirCapSeq-VERT) was used to identify norovirus in environmental samples. Family-specific viral contigs were classified and sorted by SLIM and final norovirus contigs were genotyped using the online Norovirus genotyping tool v2.0. From sewage samples, 14 norovirus genogroup I sequences were identified of which six were complete genomes. For norovirus genogroup II, nine sequences were identified and three of them comprised more than half of the genome. In oyster samples bioaccumulated with these sewage samples, only the use of an enrichment step during library preparation allowed successful identification of nine different sequences of norovirus genogroup I and four for genogroup II (>500 bp). This study demonstrates the importance of method development to increase virus recovery, and the interest of a capture-based approach to be able to identify viruses present at low concentrations.

Foodborne viruses: Detection, risk assessment, and control options in food processing

In a recent report by risk assessment experts on the identification of food safety priorities using the Delphi technique, foodborne viruses were recognized among the top rated food safety priorities and have become a greater concern to the food industry over the past few years. Food safety experts agreed that control measures for viruses throughout the food chain are required. However, much still needs to be understood with regard to the effectiveness of these controls and how to properly validate their performance, whether it is personal hygiene of food handlers or the effects of processing of at risk foods or the interpretation and action required on positive virus test result. This manuscript provides a description of foodborne viruses and their characteristics, their responses to stress and technologies developed for viral detection and control. In addition, the gaps in knowledge and understanding, and future perspectives on the application of viral detection and control strategies for the food industry, along with suggestions on how the food industry could implement effective control strategies for viruses in foods. The current state of the science on epidemiology, public health burden, risk assessment and management options for viruses in food processing environments will be highlighted in this review.

Occurrence of Bacterial Pathogens and Human Noroviruses in Shellfish-Harvesting Areas and Their Catchments in France

During a 2-year study, the presence of human pathogenic bacteria and noroviruses was investigated in shellfish, seawater and/or surface sediments collected from three French coastal shellfish-harvesting areas as well as in freshwaters from the corresponding upstream catchments. Bacteria isolated from these samples were further analyzed. Escherichia coli isolates classified into the phylogenetic groups B2, or D and enterococci from Enterococcus faecalis and E. faecium species were tested for the presence of virulence genes and for antimicrobial susceptibility. Salmonella members were serotyped and the most abundant serovars (Typhimurium and its monophasic variants and Mbandaka) were genetically characterized by high discriminative subtyping methods. Campylobacter and Vibrio were identified at the species level, and haemolysin-producing Vibrio parahaemolyticus were searched by tdh- and trh- gene detection. Main results showed a low prevalence of Salmonella in shellfish samples where only members of S. Mbandaka were found. Campylobacter were more frequently isolated than Salmonella and a different distribution of Campylobacter species was observed in shellfish compared to rivers, strongly suggesting possible additional inputs of bacteria. Statistical associations between enteric bacteria, human noroviruses (HuNoVs) and concentration of fecal indicator bacteria revealed that the presence of Salmonella was correlated with that of Campylobacter jejuni and/or C. coli as well as to E. coli concentration. A positive correlation was also found between the presence of C. lari and the detection of HuNoVs. This study highlights the importance of simultaneous detection and characterization of enteric and marine pathogenic bacteria and human noroviruses not only in shellfish but also in catchment waters for a hazard assessment associated with microbial contamination of shellfish.

Virus Type-Specific Removal in a Full-Scale Membrane Bioreactor Treatment Process

We investigated removal of noroviruses, sapoviruses, and rotaviruses in a full-scale membrane bioreactor (MBR) plant by monitoring virus concentrations in wastewater samples during two gastroenteritis seasons and evaluating the adsorption of viruses to mixed liquor suspended solids (MLSS). Sapoviruses and rotaviruses were detected in 25% of MBR effluent samples with log reduction values of 3- and 2-logs in geometric mean concentrations, respectively, while noroviruses were detected in only 6% of the samples. We found that norovirus and sapovirus concentrations in the solid phase of mixed liquor samples were significantly higher than in the liquid phase (P < 0.01, t test), while the concentration of rotaviruses was similar in both phases. The efficiency of adsorption of the rotavirus G1P[8] strain to MLSS was significantly less than norovirus GI.1 and GII.4 and sapovirus GI.2 strains (P < 0.01, t test). Differences in the adsorption of viruses to MLSS may cause virus type-specific removal during the MBR treatment process as shown by this study.

Infectivity and RNA Persistence of a Norovirus Surrogate, the Tulane Virus, in Oysters

Oysters, being filter feeders, can accumulate some human pathogens such as norovirus, a highly infectious calicivirus, most common cause of acute gastroenteritis worldwide. Accumulated virus decays over a period of days to weeks, possibly rendering contaminated oysters safe again. Sensitive molecular methods have been set up for shellfish analysis but without answering the question of infectious virus detection. Using the Tulane virus (TV), a norovirus surrogate that recognizes the same ligand as human norovirus in oyster tissues, the genome and infectious virus decay rates were estimated using inverse linear regression in a Bayesian framework for genome copies. Infectivity decreased faster than genome copies but infectious viruses were detected for several days. Quantifying the decrease in viral infectivity and genome detection in oysters over such a long period may help local authorities to manage production areas implicated in shellfish-borne outbreaks, and thus protect consumers.

Digital PCR for Quantifying Norovirus in Oysters Implicated in Outbreaks, France

Using samples from oysters clearly implicated in human disease, we quantified norovirus levels by using digital PCR. Concentrations varied from 43 to 1,170 RNA copies/oyster. The analysis of frozen samples from the production area showed the presence of norovirus 2 weeks before consumption.

Optimization of PMAxx pretreatment to distinguish between human norovirus with intact and altered capsids in shellfish and sewage samples

Shellfish contamination by human noroviruses (HuNoVs) is a serious health and economic problem. Recently an ISO procedure based on RT-qPCR for the quantitative detection of HuNoVs in shellfish has been issued, but these procedures cannot discriminate between inactivated and potentially infectious viruses. The aim of the present study was to optimize a pretreatment using PMAxx to better discriminate between intact and heat-treated HuNoVs in shellfish and sewage. To this end, the optimal conditions (30min incubation with 100μM of PMAxx and 0.5% of Triton, and double photoactivation) were applied to mussels, oysters and cockles artificially inoculated with thermally-inactivated (99°C for 5min) HuNoV GI and GII. This pretreatment reduced the signal of thermally-inactivated HuNoV GI in cockles and HuNoV GII in mussels by >3 log. Additionally, this pretreatment reduced the signal of thermally-inactivated HuNoV GI and GII between 1 and 1.5 log in oysters. Thermal inactivation of HuNoV GI and GII in PBS, sewage and bioaccumulated oysters was also evaluated by the PMAxx-Triton pretreatment. Results showed significant differences between reductions observed in the control and PMAxx-treated samples in PBS following treatment at 72 and 95°C for 15min. In sewage, the RT-qPCR signal of HuNoV GI was completely removed by the PMAxx pretreatment after heating at 72 and 95°C, while the RT-qPCR signal for HuNoV GII was completely eliminated only at 95°C. Finally, the PMAxx-Triton pretreatment was applied to naturally contaminated sewage and oysters, resulting in most of the HuNoV genomes quantified in sewage and oyster samples (12 out of 17) corresponding to undamaged capsids. Although this procedure may still overestimate infectivity, the PMAxx-Triton pretreatment represents a step forward to better interpret the quantification of intact HuNoVs in complex matrices, such as sewage and shellfish, and it could certainly be included in the procedures based on RT-qPCR.

Sustained fecal-oral human-to-human transmission following a zoonotic event

Bacterial, viral and parasitic zoonotic pathogens that transmit via the fecal-oral route have a major impact on global health. However, the mechanisms underlying the emergence of such pathogens from the animal reservoir and their persistence in the human population are poorly understood. Here, we present a framework of human-to-human transmission of zoonotic pathogens that considers the factors relevant for fecal-oral human-to-human transmission route at the levels of host, pathogen, and environment. We discuss current data gaps and propose future research directions.

Detection of Hepatitis E Virus in Sewage After an Outbreak on a French Island

A hepatitis E outbreak, which occurred on a small isolated island, provided an opportunity to evaluate the association between the number of hepatitis E cases in the community and the concentration of virus detected in sewage. Samples were collected from the different sewage treatment plants from the island and analyzed for the presence of hepatitis E (HEV) virus using real-time RT-PCR. We demonstrated that if 1-4 % of inhabitants connected to a WWTP were infected with HEV, raw sewage contained HEV at detectable levels. The finding that such a small number of infected people can contaminate municipal sewage works raises the potential of the further distribution of the virus. Indeed, investigating the routes of transmission of HEV, including the potential for sewage effluent to contain infectious HEV, may help us to better understand the epidemiology of this pathogen, which is considered to be an emerging concern in Europe.

Retention of Rotavirus Infectivity in Mussels Heated by Using the French Recipe Moules Marinières

To evaluate the persistence of infectious virus after heating, mussels contaminated with a rotavirus strain were prepared following the French recipe moules marinières (mariner's mussels). Rotavirus was then quantified by real-time quantitative PCR (RT-qPCR) and a cell culture infectivity assay. Results showed the persistence of infectious virus after 3 min of cooking. After 5 min, when no infectious virus could be detected, the RT-qPCR approach showed a 1-log decrease compared with concentrations detected after 1 min of cooking.

High Proportion of Asymptomatic Infections in an Outbreak of Hepatitis E Associated With a Spit-Roasted Piglet, France, 2013

BACKGROUND

On 11 December 2013, 3 clustered cases of hepatitis E were reported on a French coastal island. Individuals had taken part in a wedding meal that included a spit-roasted piglet. The piglet had been stuffed with a raw stuffing partly made from the liver. Investigations were carried out to identify the vehicle of contamination and evaluate the dispersion of the hepatitis E virus (HEV) in the environment.

METHODS

A questionnaire was administered to 98 wedding participants who were asked to give a blood sample. Cases were identified by reverse transcription-polymerase chain reaction and serological tests. A retrospective cohort study was conducted among 38 blood-sampled participants after the exclusion of 14 participants with evidence of past HEV infection. Relative risks (RR) and 95% confidence intervals were calculated based on food consumed at the wedding meal using univariate and multivariable Poisson regressions. Phylogenetic analyses were performed to compare the clinical HEV strains. Strains were detected in the liquid manure sampled at the farm where the piglet was born and in the untreated island wastewater.

RESULTS

Seventeen cases were identified, 70.6% were asymptomatic. Acute HEV infection was independently associated with piglet stuffing consumption (RR = 1.69 [1.04-2.73], P = .03). Of clinical strains from the index cases, veterinary and environmental HEV strains were identical.

CONCLUSIONS

Our investigation attributed this large HEV outbreak to the consumption of an undercooked pig liver-based stuffing. After infection, the cases became a temporary reservoir for HEV, which was detected in the island's untreated wastewater.

Multiplex real-time RT-PCR for the simultaneous detection and quantification of GI, GII and GIV noroviruses

Noroviruses are important causes of acute gastroenteritis and are classified into six genogroups with GI, GII and GIV containing human pathogens. This high genetic diversity represents a significant challenge for diagnostic assay development. Genogroup specific monoplex and multiplex real time RT-PCR assays are widely used for the detection of GI and GII noroviruses. On the other hand, GIV norovirus detection is not part of routine laboratory diagnosis. This study describes the development and evaluation of a one tube, real time RT-PCR assay for the simultaneous detection and quantification of GI, GII and GIV noroviruses, including both GIV.1 (human) and GIV.2 (animal) strains. Assay performance was evaluated on a panel of norovirus positive clinical samples by comparison of monoplex and multiplex standard curves and Ct values. The multiplex assay demonstrated equal sensitivity and specificity to the monoplex assays and was able to detect all GI, GII and GIV noroviruses with Ct values equal to that of the monoplex assays. The multiplex assay described in this study will be instrumental for the better understanding of GIV norovirus epidemiology, including their possible zoonotic nature.

Tulane Virus as a Potential Surrogate To Mimic Norovirus Behavior in Oysters

Oyster contamination by noroviruses is an important health and economic problem. The present study aimed to compare the behaviors of Norwalk virus (the prototype genogroup I norovirus) and two culturable viruses: Tulane virus and mengovirus. After bioaccumulation, tissue distributions were quite similar for Norwalk virus and Tulane virus, with the majority of viral particles detected in digestive tissues, while mengovirus was detected in large amounts in the gills and mantle as well as in digestive tissues. The levels of persistence of all three viruses over 8 days were comparable, but clear differences were observed over longer periods, with Norwalk and Tulane viruses displaying rather similar half-lives, unlike mengovirus, which was cleared more rapidly. These results indicate that Tulane virus may be a good surrogate for studying norovirus behavior in oysters, and they confirm the prolonged persistence of Norwalk virus in oyster tissues.

Bioaccumulation efficiency, tissue distribution, and environmental occurrence of hepatitis E virus in bivalve shellfish from France

Hepatitis E virus (HEV), an enteric pathogen of both humans and animals, is excreted by infected individuals and is therefore present in wastewaters and coastal waters. As bivalve molluscan shellfish are known to concentrate viral particles during the process of filter feeding, they may accumulate this virus. The bioaccumulation efficiencies of oysters (Crassostrea gigas), flat oysters (Ostrea edulis), mussels (Mytilus edulis), and clams (Ruditapes philippinarum) were compared at different time points during the year. Tissue distribution analysis showed that most of the viruses were concentrated in the digestive tissues of the four species. Mussels and clams were found to be more sensitive to sporadic contamination events, as demonstrated by rapid bioaccumulation in less than 1 h compared to species of oysters. For oysters, concentrations increased during the 24-h bioaccumulation period. Additionally, to evaluate environmental occurrence of HEV in shellfish, an environmental investigation was undertaken at sites potentially impacted by pigs, wild boars, and human waste. Of the 286 samples collected, none were contaminated with hepatitis E virus, despite evidence that this virus is circulating in some French areas. It is possible that the number of hepatitis E viral particles discharged into the environment is too low to detect or that the virus may have a very short period of persistence in pig manure and human waste.

Environmental detection of genogroup I, II, and IV noroviruses by using a generic real-time reverse transcription-PCR assay

Norovirus is the most common agent implicated in food-borne outbreaks and is frequently detected in environmental samples. These viruses are highly diverse, and three genogroups (genogroup I [GI], GII, and GIV) infect humans. Being noncultivable viruses, real-time reverse transcription-PCR (RT-PCR) is the only sensitive method available for their detection in food or environmental samples. Selection of consensus sequences for the design of sensitive assays has been challenging due to sequence diversity and has led to the development of specific real-time RT-PCR assays for each genogroup. Thus, sample screening can require several replicates for amplification of each genogroup (without considering positive and negative controls or standard curves). This study reports the development of a generic assay that detects all three human norovirus genogroups on a qualitative basis using a one-step real-time RT-PCR assay. The generic assay achieved good specificity and sensitivity for all three genogroups, detected separately or in combination. At variance with multiplex assays, the choice of the same fluorescent dye for all three probes specific to each genogroup allows the levels of fluorescence to be added and may increase assay sensitivity when multiple strains from different genogroups are present. When it was applied to sewage sample extracts, this generic assay successfully detected norovirus in all samples found to be positive by the genogroup-specific RT-PCRs. The generic assay also identified all norovirus-positive samples among 157 archived nucleic acid shellfish extracts, including samples contaminated by all three genogroups.

Oysters and norovirus: something special?

Shellfish can be a vector for human pathogens. Despite regulation based on enteric bacteria, shellfish are still implicated in viral outbreaks. Oysters are the most common shellfish associated with outbreaks, and noroviruses, which cause acute gastroenteritis, are the most frequently identified pathogen in these outbreaks. Analysis of shellfish-related outbreak data worldwide shows an unexpected high proportion of genogroup I strains. Recent studies performed in vitro, in vivo and in the environment indicate that oysters are not just a passive filter, but can selectively accumulate norovirus strains based on virus carbohydrate ligands shared with humans. These observations may help explain the GI/GII bias observed in shellfish-related outbreaks compared to other outbreaks.

Chronic or accidental exposure of oysters to norovirus: is there any difference in contamination?

Bivalve molluscan shellfish such as oysters may be contaminated by human pathogens. Currently, the primary pathogens associated with shellfish-related outbreaks are noroviruses. This study was conducted to improve understanding of oyster bioaccumulation when oysters were exposed to daily contamination or one accidental contamination event, i.e., different modes of contamination. Oysters were contaminated with two representative strains of norovirus (GI.1 and GII.3) and then analyzed with real-time reverse transcription PCR. Exposure to a repeated virus dose for 9 days (mimicking a growing area subjected to frequent sewage contamination) led to an additive accumulation that was not significantly different from that obtained when the same total dose of virus was added all at once (as may happen after accidental sewage discharge). Similarly, bioaccumulation tests performed with mixed strains revealed additive accumulation of both viruses. Depuration may not be efficient for eliminating viruses; therefore, to prevent contaminated shellfish from being put onto the market, continuous sanitary monitoring must be considered. All climatic events or sewage failures occurring in production areas must be recorded, because repeated low-dose exposure or abrupt events may lead to similar levels of accumulation. This study contributes to an understanding of norovirus accumulation in oysters and provides suggestions for risk management strategies.

Norovirus and other human enteric viruses in moroccan shellfish

The aim of this study was to evaluate the presence of human enteric viruses in shellfish collected along the Mediterranean Sea and Atlantic Coast of Morocco. A total of 77 samples were collected from areas potentially contaminated by human sewage. Noroviruses were detected in 30 % of samples, with an equal representation of GI and GII strains, but were much more frequently found in cockles or clams than in oysters. The method used, including extraction efficiency controls, allowed the quantification of virus concentration. As in previous reports, results showed levels of contamination between 100 and 1,000 copies/g of digestive tissues. Sapoviruses were detected in 13 % of samples mainly in oyster and clam samples. Hepatitis A virus was detected in two samples, with concentrations around 100 RNA copies/g of digestive tissues. Only two samples were contaminated with enterovirus and none with norovirus GIV or Aichi virus. This study highlights the interest of studying shellfish samples from different countries and different production areas. A better knowledge of shellfish contamination helps us to understand virus levels in shellfish and to improve shellfish safety, thus protecting consumers.

Infectivity of GI and GII noroviruses established from oyster related outbreaks

Noroviruses (NoVs) are the major cause of acute epidemic gastroenteritis in industrialized countries. Outbreak strains are predominantly genogroup II (GII) NoV, but genogroup I (GI) strains are regularly found in oyster related outbreaks. The prototype Norwalk virus (GI), has been shown to have high infectivity in a human challenge study. Whether other NoVs are equally infectious via natural exposure remains to be established. Human susceptibility to NoV is partly determined by the secretor status (Se+/-). Data from five published oyster related outbreaks were analyzed in a Bayesian framework. Infectivity estimates where high and consistent with NV(GI) infectivity, for both GII and GI strains. The median and CI95 probability of infection and illness, in Se+ subjects, associated with exposure to a mean of one single NoV genome copy were around 0.29[0.015-0.61] for GI and 0.4[0.04-0.61] for GII, and for illness 0.13[0.007-0.39] for GI and 0.18[0.017-0.42] for GII. Se- subjects were strongly protected against infection. The high infectivity estimates for Norwalk virus GI and GII, makes NoVs critical target for food safety regulations.

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.

Assessment of human enteric viruses in cultured and wild bivalve molluscs

Standard and real-time reverse transcription-PCR (rRT-PCR) procedures were used to monitor cultured and wild bivalve molluscs from the Ría de Vigo (NW Spain) for the main human enteric RNA viruses, specifically, norovirus (NoV), hepatitis A virus (HAV), astrovirus (AsV), rotavirus (RT), enterovirus (EV), and Aichi virus (AiV). The results showed the presence of at least one enteric virus in 63.4% of the 41 samples analyzed. NoV GII was the most prevalent virus, detected in 53.7% of the samples, while NoV GI, AsV, EV, and RV were found at lower percentages (7.3, 12.2, 12.2, and 4.9%, respectively). In general, samples obtained in the wild were more frequently contaminated than those from cultured (70.6 vs. 58.3%) molluscs and were more readily contaminated with more than one virus. However, NoV GI was detected in similar amounts in cultured and wild samples (6.4 x 10(2) to 3.3 x 10(3) RNA copies per gram of digestive tissue) while the concentrations of NoV GII were higher in cultured (from 5.6 x 10(1) to 1.5 x 10(4) RNA copies per gram of digestive tissue) than in wild (from 1.3 x 10(2) to 3.4 x 10(4) RNA copies per gram of digestive tissue) samples.

Detection and quantification of noroviruses in shellfish

Noroviruses (NoVs) are the most common viral agents of acute gastroenteritis in humans, and high concentrations of NoVs are discharged into the environment. As these viruses are very resistant to inactivation, the sanitary consequences are contamination of food, including molluscan shellfish. There are four major problems with NoV detection in shellfish samples: low levels of virus contamination, the difficulty of efficient virus extraction, the presence of interfering substances that inhibit molecular detection, and NoV genetic variability. The aims of this study were to adapt a kit for use with a method previously shown to be efficient for detection of NoV in shellfish and to use a one step real-time reverse transcription-PCR method with addition of an external viral control. Comparisons of the two methods using bioaccumulated oysters showed that the methods reproducibly detected similar levels of virus in oyster samples. Validation studies using naturally contaminated samples also showed that there was a good correlation between the results of the two methods, and the variability was more attributable to the level of sample contamination. Magnetic silica very efficiently eliminated inhibitors, and use of extraction and amplification controls increased quality assurance. These controls increased the confidence in estimates of NoV concentrations in shellfish samples and strongly supported the conclusion that the results of the method described here reflected the levels of virus contamination in oysters. This approach is important for food safety and is under evaluationfor European regulation.

Norovirus removal and particle association in a waste stabilization pond

The presence of norovirus (NoV) genogroup I (GI) and II (GII) was evaluated using real-time reverse transcription polymerase chain reaction (rRT-PCR) in the influent, two midtreatment locations, and final effluent of a three-pond serial waste stabilization pond system from December 2005 through June 2006. Additionally, influent and effluent samples were filtered through a cascade of three membrane filters with sequentially smaller pores to determine the size range of particles with which GI and GII were associated. NoV GI and GII removal occurs primarily in the third pond. Viruses were found on large settleable particles (retained on a 180 microm filter), on smaller suspended particles (retained on a 0.45 microm filter), on colloidal particles (retained on a positively charged 0.45 microm filter), and in the final filtrate. Both GI and GII in influent samples were found to be dominantly associated with particles smaller than 180 microm, thereby suggesting that particle settling is not the main virus removal mechanism in the waste stabilization pond system. On average, NoV detected in filtered effluent samples were associated with particles between 0.45 and 180 microm in diameter (47 and 67% of detected GI and GII, respectively). The presence of NoV GI and GII in the final filtrate of influent and effluent samples shows that positively charged membrane filters often used for viral concentration methods are not capable of trapping all viruses present in wastewater samples.

Rapid virus detection procedure for molecular tracing of shellfish associated with disease outbreaks

Detection of pathogenic viruses in oysters implicated in gastroenteritis outbreaks is often hampered by time-consuming, specialist virus extraction methods. Five virus RNA extraction methods were evaluated with respect to performance characteristics and sensitivity on artificially contaminated oyster digestive glands. The two most promising procedures were further evaluated on bioaccumulated and naturally contaminated oysters. The most efficient method was used to trace the source in an outbreak situation. Out of five RNA extraction protocols, PEG precipitation and the RNeasy Kit performed best with norovirus genogroup III-spiked digestive glands. Analyzing 24-h bioaccumulated oysters revealed a slightly better sensitivity with PEG precipitation, but the RNeasy Kit was less prone to concentrate inhibitors. The latter procedure demonstrated the presence of human noroviruses in naturally contaminated oysters and oysters implicated in an outbreak. In this outbreak, in four out of nine individually analyzed digestive glands, norovirus was detected. In one of the oysters and in one of the fecal samples of the clinical cases, identical norovirus strains were detected. A standard and rapid virus extraction method using the RNeasy Kit appeared to be most useful in tracing shellfish as the source in gastroenteritis outbreaks, and to be able to make effective and timely risk management decisions.

Detection of multiple noroviruses associated with an international gastroenteritis outbreak linked to oyster consumption

An international outbreak linked to oyster consumption involving a group of over 200 people in Italy and 127 total subjects in 13 smaller clusters in France was analyzed using epidemiological and clinical data and shellfish samples. Environmental information from the oyster-producing area, located in a lagoon in southern France, was collected to investigate the possible events leading to the contamination. Virologic analyses were conducted by reverse transcription-PCR (RT-PCR) using the same primer sets for both clinical and environmental samples. After sequencing, the data were analyzed through the database operated by the scientific network FoodBorne Viruses in Europe. The existence of an international collaboration between laboratories was critical to rapidly connect the data and to fully interpret the results, since it was not obvious that one food could be the link because of the diversity of the several norovirus strains involved in the different cases. It was also demonstrated that heavy rain was responsible for the accidental contamination of seafood, leading to a concentration of up to hundreds of genomic copies per oyster as detected by real-time RT-PCR.

Human and animal enteric caliciviruses in oysters from different coastal regions of the United States

Food-borne diseases are a major cause of morbidity and hospitalization worldwide. Enteric caliciviruses are capable of persisting in the environment and in the tissues of shellfish. Human noroviruses (HuNoVs) have been implicated in outbreaks linked to shellfish consumption. The genetic and antigenic relatedness between human and animal enteric caliciviruses suggests that interspecies transmission may occur. To determine the occurrence of human and animal enteric caliciviruses in United States market oysters, we surveyed regional markets. Oysters were collected from 45 bays along the United States coast during the summer and winter of 2002 and 2003. Samples were analyzed by reverse transcription-PCR, and results were confirmed by hybridization and sequence analysis. Nine samples (20%) were positive for HuNoV genogroup II after hybridization. Animal enteric caliciviruses were detected in 10 samples (22%). Seven of these samples were positive for porcine norovirus genogroup II, and one sample was positive for porcine sapovirus after hybridization and confirmation by sequencing. Bovine noroviruses were detected in two samples, and these results were confirmed by sequencing. Five HuNoV samples sequenced in the polymerase region were similar to the norovirus genogroup II US 95/96 subset (genogroup II-4) previously implicated in diarrhea outbreaks. Different seasonal and state distributions were detected. The presence of animal enteric caliciviruses was associated with states with high livestock production. Although the presence of human caliciviruses in raw oysters represents a potential risk for gastroenteritis, disease confirmation by investigation of outbreaks is required. The simultaneous detection of human and animal enteric caliciviruses raises concerns about human infection or coinfection with human and animal strains that could result in genomic recombination and the emergence of new strains.

Use of rotavirus virus-like particles as surrogates to evaluate virus persistence in shellfish

Rotavirus virus-like particles (VLPs) and MS2 bacteriophages were bioaccumulated in bivalve mollusks to evaluate viral persistence in shellfish during depuration and relaying under natural conditions. Using this nonpathogenic surrogate virus, we were able to demonstrate that about 1 log10 of VLPs was depurated after 1 week in warm seawater (22 degrees C). Phage MS2 was depurated more rapidly (about 2 log10 in 1 week) than were VLPs, as determined using a single-compartment model and linear regression analysis. After being relayed in the estuary under the influence of the tides, VLPs were detected in oysters for up to 82 days following seeding with high levels of VLPs (concentration range between 10(10) and 10(9) particles per g of pancreatic tissue) and for 37 days for lower contamination levels (10(5) particles per g of pancreatic tissue). These data suggest that viral particles may persist in shellfish tissues for several weeks.

Detection of noroviruses in raspberries associated with a gastroenteritis outbreak

Following an acute foodborne gastroenteritis outbreak in southern Sweden, stool specimens from five of nine ill patients were found positive for norovirus using reverse transcriptase polymerase chain reaction. Epidemiological data pointed to raspberry cakes as the source of the outbreak. Using a combination of generic and patient-specific primers and novel food analysis methodology (with extraction efficiency control and inhibitor removal), norovirus strains from two different genogroups were directly identified in the contaminated raspberries.

Rotavirus VLP2/6: a new tool for tracking rotavirus in the marine environment

The potential of rotavirus 2/6-virus-like-particles (VLP2/6) for use as tracers in the marine environment was investigated. The stability of bovine rotavirus (strain RF) and VLP2/6 in natural seawater at 25 degrees C for six days was studied. ELISA and western blot methods were used to quantify the particles. The rates of decline of rotavirus particles and VLP2/6 were similar (approximately 0.5log(10) per day). Western blot analysis showed that the integrity of capsid proteins VP2 and VP6 was conserved during the incubation time. These results demonstrate that VLP2/6 particles have the same stability in seawater as rotavirus particles. Thus, VLP2/6 can be used as a tracer, which should be of particular value for studying the fate of rotavirus particles in the marine environment.