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At this time, about 3,000 different viruses are recognized, but metagenomic studies suggest that these viruses are a small fraction of the viruses that exist in nature. We have explored viral diversity by deep sequencing nucleic acids obtained from virion populations enriched from raw sewage. We identified 234 known viruses, including 17 that infect humans. Plant, insect, and algal viruses as well as bacteriophages were also present. These viruses represented 26 taxonomic families and included viruses with single-stranded DNA (ssDNA), double-stranded DNA (dsDNA), positive-sense ssRNA [ssRNA(+)], and dsRNA genomes. Novel viruses that could be placed in specific taxa represented 51 different families, making untreated wastewater the most diverse viral metagenome (genetic material recovered directly from environmental samples) examined thus far. However, the vast majority of sequence reads bore little or no sequence relation to known viruses and thus could not be placed into specific taxa. These results show that the vast majority of the viruses on Earth have not yet been characterized. Untreated wastewater provides a rich matrix for identifying novel viruses and for studying virus diversity.Importance At this time, virology is focused on the study of a relatively small number of viral species. Specific viruses are studied either because they are easily propagated in the laboratory or because they are associated with disease. The lack of knowledge of the size and characteristics of the viral universe and the diversity of viral genomes is a roadblock to understanding important issues, such as the origin of emerging pathogens and the extent of gene exchange among viruses. Untreated wastewater is an ideal system for assessing viral diversity because virion populations from large numbers of individuals are deposited and because raw sewage itself provides a rich environment for the growth of diverse host species and thus their viruses. These studies suggest that the viral universe is far more vast and diverse than previously suspected.

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Food safety criteria for Listeria monocytogenes in ready-to-eat (RTE) foods have been applied from 2006 onwards (Commission Regulation (EC) 2073/2005. Still, human invasive listeriosis was reported to increase over the period [2009][2010][2011][2012][2013] in the European Union and European Economic Area (EU/EEA). Time series analysis for the 2008-2015 period in the EU/EEA indicated an increasing trend of the monthly notified incidence rate of confirmed human invasive listeriosis of the over 75 age groups and female age group between 25 and 44 years old (probably related to pregnancies). A conceptual model was used to identify factors in the food chain as potential drivers for L. monocytogenes contamination of RTE foods and listeriosis. Factors were related to the host (i. population size of the elderly and/or susceptible people; ii. underlying condition rate), the food (iii. L. monocytogenes prevalence in RTE food at retail; iv. L. monocytogenes concentration in RTE food at retail; v. storage conditions after retail; vi. consumption), the national surveillance systems (vii. improved surveillance), and/or the bacterium (viii. virulence). Factors considered likely to be responsible for the increasing trend in cases are the increased population size of the elderly and susceptible population except for the 25-44 female age group. For the increased incidence rates and cases, the likely factor is the increased proportion of susceptible persons in the age groups over 45 years old for both genders. Quantitative modelling suggests that more than 90% of invasive listeriosis is caused by ingestion of RTE food containing > 2,000 colony forming units (CFU)/g, and that one-third of cases are due to growth in the consumer phase. Awareness should be increased among stakeholders, especially in relation to susceptible risk groups. Innovative methodologies including whole genome sequencing (WGS) for strain identification and monitoring of trends are recommended. Acknowledgements: The Panel wishes to thank the hearing experts: Andrew Hart and Sophie Roussel for the support provided to this scientific output. The Panel also wishes to thank the consortia of the three outsourcing activities under 'Closing gaps for performing a risk assessment on L. monocytogenes in RTE foods' for their collaboration. In addition, R egis Pouillot is thanked for sharing the dose response model as described in Pouillot et al. (2015). Also the epidemiologists and microbiologists of the nominated public health contact points for listeriosis and Listeria isolates in the European Food-and Waterborne Diseases and Zoonoses network (FWD-Net) are thanked for replying to the questionnaire related to the surveillance of listeriosis.

To determine the prevalence of Hepatitis E virus (HEV) in industrialized nations, we analyzed the excretion of HEV strains by the populations of Spain, France, Greece, Sweden, and the United States. Twenty of 46 (43.5%) urban sewage samples collected in Barcelona from 1994 to 2002 tested positive for HEV. We identified 15 HEV strains, which were similar to two HEV isolates previously described in Barcelona in clinical samples and to strains from diverse geographic HEV-nonendemic areas. We also identified two HEV strains in sewage samples from Washington, D.C., and Nancy, France; these samples were also positive for Hepatitis A virus. In addition, we studied the role of pigs as a reservoir for HEV and identified one new swine HEV strain. Our results suggest that HEV may be more prevalent than previously considered in industrialized countries and that variants of the virus circulate simultaneously in one region.