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

Type Article
Date 2020-09
Language English
Author(s) Desdouits MarionORCID1, Wacrenier Candice1, Ollivier Joanna1, Schaeffer Julien1, Le Guyader Soizick1
Affiliation(s) 1 : Laboratoire de Microbiologie (LSEM), Ifremer, rue de l’Ile d’Yeu, B.P. 21105, CEDEX 03, 44311 Nantes, France
Source Viruses-basel (1999-4915) (MDPI AG), 2020-09 , Vol. 12 , N. 9 , P. 978 (17p.)
DOI 10.3390/v12090978
WOS© Times Cited 6
Keyword(s) norovirus, foodborne virus, metagenomics, amplicon deep sequencing, viral diversity

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.

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Desdouits Marion, Wacrenier Candice, Ollivier Joanna, Schaeffer Julien, Le Guyader Soizick (2020). A Targeted Metagenomics Approach to Study the Diversity of Norovirus GII in Shellfish Implicated in Outbreaks. Viruses-basel, 12(9), 978 (17p.). Publisher's official version : https://doi.org/10.3390/v12090978 , Open Access version : https://archimer.ifremer.fr/doc/00646/75831/