ArticleFrontiers in microbiology2019
Metavirome Sequencing to Evaluate Norovirus Diversity in Sewage and Related Bioaccumulated Oysters.
Article in Frontiers in microbiology, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 20 papers.
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Who cites it
20 citing papers in PubMed, 37 citations in OpenAlex.
- Evaluation of two virome probe hybridization capture panels for food safety surveillance.Virology journal · 2026Article
- A Metagenomic Survey of Virological Hazards in Market-Ready Oysters.Food and environmental virology · 2025Article
- Long Amplicon Nanopore Sequencing for Dual-Typing RdRp and VP1 Genes of Norovirus Genogroups I and II in Wastewater.Food and environmental virology · 2024Article
- Viruses in Wastewater-A Concern for Public Health and the Environment.Microorganisms · 2024Review
- Whole-Genome Sequencing-Based Confirmatory Methods on RT-qPCR Results for the Detection of Foodborne Viruses in Frozen Berries.Food and environmental virology · 2024Article
- Evaluation of the Impact of Concentration and Extraction Methods on the Targeted Sequencing of Human Viruses from Wastewater.Environmental science & technology · 2024Article
- Grey and harbor seals in France (mainland and Saint-Pierre et Miquelon): microbial communities and identification of a microbial source tracking seal marker.Frontiers in microbiology · 2024Article
- A Comprehensive Review for the Surveillance of Human Pathogenic Microorganisms in Shellfish.Microorganisms · 2023Review
- Exploring the Astrovirome of Shellfish Matrices Using Nanopore Sequencing.Veterinary sciences · 2023Article
- Next Generation Sequencing Approaches to Characterize the Respiratory Tract Virome.Microorganisms · 2022Review
- Clinical and In Vitro Evidence Favoring Immunoglobulin Treatment of a Chronic Norovirus Infection in a Patient With Common Variable Immunodeficiency.The Journal of infectious diseases · 2022Article
- Establishing farm dust as a useful viral metagenomic surveillance matrix.Scientific reports · 2022Article
- SARS-CoV-2 Whole-Genome Sequencing Using Oxford Nanopore Technology for Variant Monitoring in Wastewaters.Frontiers in microbiology · 2022Article
- Performance evaluation of virus concentration methods for implementing SARS-CoV-2 wastewater based epidemiology emphasizing quick data turnaround.The Science of the total environment · 2021Article
- Next-generation diagnostics: virus capture facilitates a sensitive viral diagnosis for epizootic and zoonotic pathogens including SARS-CoV-2.Microbiome · 2021Article
- High Throughput Sequencing for the Detection and Characterization of RNA Viruses.Frontiers in microbiology · 2021Review
- Human and Animal RNA Virus Diversity Detected by Metagenomics in Cameroonian Clams.Frontiers in microbiology · 2021Article
- Metagenomics-Based Proficiency Test of Smoked Salmon Spiked with a Mock Community.Microorganisms · 2020Article
- Viruses in wastewater: occurrence, abundance and detection methods.The Science of the total environment · 2020Review
- Novel opportunities for NGS-based one health surveillance of foodborne viruses.One health outlook · 2020Review
Corrections and comments
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Authors and funding
12 authors at 2 institutions in 2 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
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.
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