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Original Research ARTICLE Provisionally accepted The full-text will be published soon. Notify me

Front. Microbiol. | doi: 10.3389/fmicb.2019.02394

Metavirome sequencing to evaluate norovirus diversity in sewage and related bioaccumulated oysters.

  • 1Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER), France
  • 2Department of Viroscience, Erasmus Medical Center, Netherlands
  • 3Laboratoire de Microbiologie, Institut Français de la Mer, France

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 (>500bp). 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.

Keywords: Norovirus, Sewage, oysters, Metagenomic analysis, Metavirome

Received: 24 Jul 2019; Accepted: 03 Oct 2019.

Copyright: © 2019 Strubbia, Schaeffer, Oude Munnink, Besnard, Phan, Nieuwenhuijse, de Graaf, Schapendon, Wacrenier, Cotten, Koopmans and Le Guyader. This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) and the copyright owner(s) are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.

* Correspondence: Dr. Francoise S. Le Guyader, Institut Français de la Mer, Laboratoire de Microbiologie, Paris, France,