Occurrence and Trend of Hepatitis A Virus in Bivalve Molluscs Production Areas Following a Contamination Event

Hepatitis A Virus and Hepatitis E Virus as Food- and Waterborne Pathogens-Transmission Routes and Methods for Detection in Food

Foodborne viruses are an important threat to food safety and public health. Globally, there are approximately 5 million cases of acute viral hepatitis due to hepatitis A virus (HAV) and hepatitis E virus (HEV) every year. HAV is responsible for numerous food-related viral outbreaks worldwide, while HEV is an emerging pathogen with a global health burden. The reported HEV cases in Europe have increased tenfold in the last 20 years due to its zoonotic transmission through the consumption of infected meat or meat products. HEV is considered the most common cause of acute viral hepatitis worldwide currently. This review focuses on the latest findings on the foodborne transmission routes of HAV and HEV and the methods for their detection in different food matrices.

Benchmarking Bioinformatic Tools for Amplicon-Based Sequencing of Norovirus

In order to survey noroviruses in our environment, it is essential that both wet-lab and computational methods are fit for purpose. Using a simulated sequencing data set, denoising-based (DADA2, Deblur and USEARCH-UNOISE3) and clustering-based pipelines (VSEARCH and FROGS) were compared with respect to their ability to represent composition and sequence information. Open source classifiers (Ribosomal Database Project [RDP], BLASTn, IDTAXA, QIIME2 naive Bayes, and SINTAX) were trained using three different databases: a custom database, the NoroNet database, and the Human calicivirus database. Each classifier and database combination was compared from the perspective of their classification accuracy. VSEARCH provides a robust option for analyzing viral amplicons based on composition analysis; however, all pipelines could return OTUs with high similarity to the expected sequences. Importantly, pipeline choice could lead to more false positives (DADA2) or underclassification (FROGS), a key aspect when considering pipeline application for source attribution. Classification was more strongly impacted by the classifier than the database, although disagreement increased with norovirus GII.4 capsid variant designation. We recommend the use of the RDP classifier in conjunction with VSEARCH; however, maintenance of the underlying database is essential for optimal use. IMPORTANCE In benchmarking bioinformatic pipelines for analyzing high-throughput sequencing (HTS) data sets, we provide method standardization for bioinformatics broadly and specifically for norovirus in situations for which no officially endorsed methods exist at present. This study provides recommendations for the appropriate analysis and classification of norovirus amplicon HTS data and will be widely applicable during outbreak investigations.

Quantitative Real-Time PCR and Digital PCR to Evaluate Residual Quantity of HAV in Experimentally Depurated Mussels

Kinetics of hepatitis A virus (HAV) accumulation and depuration from mussels (Mytilus galloprovincialis) was studied in an experimental depuration system. Different parameters likely to influence the rate of virus accumulation and elimination were evaluated. Analyses were carried out by both real-time RT-qPCR and digital PCR. Results demonstrated that the animals start to concentrate the virus already after one hour and reach the maximum level of contamination in 6 h of experiment. With respect to depuration, HAV showed a rapid reduction of the concentration (89%) during the first 24-48 h of experiment and a very slow virus decrement in the following days with a 1% residual RNA at the ninth day of depuration. When process parameters likely to increase the depuration rate (presence of ozone, microalgal feeding, presence of lactic bacteria, pre-treatment with digestive enzymes) were tested, no significant differences in the kinetics were observed. Only treatment with pancreatin seemed to positively affect depuration in the first two days of the experiment.

Foodborne transmission of hepatitis A and hepatitis E viruses: A literature review

Foodborne viruses have been recognized as a growing concern to the food industry and a serious public health problem. Hepatitis A virus (HAV) is responsible for the majority of viral outbreaks of food origin worldwide, while hepatitis E virus (HEV) has also been gaining prominence as a foodborne viral agent in the last years, due to its zoonotic transmission through the consumption of uncooked or undercooked infected meat or derivatives. However, there is a lack of scientific reports that gather all the updated information about HAV and HEV as foodborne viruses. A search of all scientific articles about HAV and HEV in food until March 2020 was carried out, using the keywords "HAV", "HEV", "foodborne", "outbreak" and "detection in food". Foodborne outbreaks due to HAV have been reported since 1956, mainly in the USA, and in Europe in recent years, where the number of outbreaks has been increasing throughout time, and nowadays it has become the continent with the highest foodborne HAV outbreak report. Investigation and detection of HAV in food is more recent, and the first detections were performed in the 1990s decade, most of them carried out on seafood, first, and frozen food, later. On the other hand, HEV has been mainly looked for and detected in food derived from reservoir animals, such as meat, sausages and pate of pigs and wild boars. For this virus, only isolated cases and small outbreaks of foodborne transmission have been recorded, most of them in industrialized countries, due to HEV genotype 3 or 4. Virus detection in food matrices requires special processing of the food matrix, followed by RNA detection by molecular techniques. For HAV, a real-time PCR has been agreed as the standard method for virus detection in food; in the case of HEV, a consensus assay for its detection in food has not been reached yet. Our investigation shows that there is still little data about HAV and HEV prevalence and frequency of contamination in food, prevalent viral strains, and sources of contamination, mainly in developing countries, where there is no research and legislation in this regard. Studies on these issues are needed to get a better understanding of foodborne viruses, their maintenance and their potential to cause diseases.

Hepatitis A Virus Strains Circulating in the Campania Region (2015-2018) Assessed through Bivalve Biomonitoring and Environmental Surveillance

The genetic diversity of Hepatitis A Virus (HAV) circulating in the Campania Region in years 2015–2018 was investigated through the monitoring of sentinel bivalve shellfish and water matrices. Overall, 463 water samples (71 sewage samples, 353 coastal discharge waters, and 39 seawaters samples), and 746 bivalve shellfish samples were analyzed. Positivity for HAV was detected in 20/71 sewage samples, 14/353 coastal discharge waters, 5/39 seawaters, and 102/746 bivalve shellfish. Sixty-one of the positive samples were successfully sequenced and were characterized as genotype IA (n = 50) and IB (n = 11). The prevalent strain circulating in 2015 in both bivalves and waters was the IA strain responsible for the outbreak occurring around the same time in the Naples area. This variant was no longer identified in subsequent years (2017–2018) when, instead, appeared two of the IA variants of the multistate outbreak affecting men who have sex with men (MSM), VRD_521_2016, and RIVM-HAV16–090, with the former prevailing in both shellfish and water environments. HAV IB isolates were detected over the years in shellfish and in water matrices, but not in clinical samples, suggesting that this genotype had been circulating silently. An integrated surveillance system (environment/food/clinical cases) can be a useful tool to monitor changes in viral variants in the population, as well as an early warning system.

Analysis of the sanitary survey 2015-2017 conducted in the gulf of La Spezia (Italy): Reclassification of the areas of production of live bivalve molluscs

The sanitary survey is aimed at classifying and monitoring the production areas of live bivalve molluscs (LBM) and it is performed using standards that are provided by the Centre for Environment, Fisheries and Aquaculture Science's Guide to Good Practice. In this study, data from the sanitary survey carried out by the Asl5 Spezzino on the production areas of the gulf of La Spezia during the period 2015-2017 were analysed. The number and type of the analysis performed both on the total sampling and on the individual target species, as well as the number and type of found non-compliance (assessed on both mandatory parameters and on parameters fixed by the local monitoring plan) were considered. Data were also compared with those from the sanitary survey 2012-2014. Appropriate statistic tests were used to evaluate data from E. coli and Norovirus monitoring. Overall, 4306 analysis were performed, especially on the species M. galloprovincialis (89%) and they were mostly focused on to the search of biological agents. 160 NC were detected. Most of the NC concerns the Norovirus's positivity (93.75%) in M. galloprovincialis and C. gigas. A correlation between the levels of E. coli and rainfall/ seasonality (higher levels in the colder months) was proved, especially in the sampling points located in the inner part of the dam and in the Portovenere Bay. Class B was reconfirmed for M. galloprovincialis, the production areas of C. gigas were reclassified as A and those of V. verrucosa were definitively closed. The sanitary survey was therefore confirmed as a useful tool for reclassification and for monitoring LBM production areas.

A Needle in A Haystack: Tracing Bivalve-Associated Viruses in High-Throughput Transcriptomic Data

Bivalve mollusks thrive in environments rich in microorganisms, such as estuarine and coastal waters, and they tend to accumulate various particles, including viruses. However, the current knowledge on mollusk viruses is mainly centered on few pathogenic viruses, whereas a general view of bivalve-associated viromes is lacking. This study was designed to explore the viral abundance and diversity in bivalve mollusks using transcriptomic datasets. From analyzing RNA-seq data of 58 bivalve species, we have reconstructed 26 nearly complete and over 413 partial RNA virus genomes. Although 96.4% of the predicted viral proteins refer to new viruses, some sequences belong to viruses associated with bivalve species or other marine invertebrates. We considered short non-coding RNAs (sncRNA) and post-transcriptional modifications occurring specifically on viral RNAs as tools for virus host-assignment. We could not identify virus-derived small RNAs in sncRNA reads obtained from the oyster sample richest in viral reads. Single Nucleotide Polymorphism (SNP) analysis revealed 938 A-to-G substitutions occurring on the 26 identified RNA viruses, preferentially impacting the AA di-nucleotide motif. Under-representation analysis revealed that the AA motif is under-represented in these bivalve-associated viruses. These findings improve our understanding of bivalve viromes, and set the stage for targeted investigations on the specificity and dynamics of identified viruses.