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| Desdouits, Marion; Wacrenier, Candice; Ollivier, Joanna; Schaeffer, Julien; Le Guyader, Soizick. |
| 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... |
| Tipo: Text |
Palavras-chave: Norovirus; Foodborne virus; Metagenomics; Amplicon deep sequencing; Viral diversity. |
| Ano: 2020 |
URL: https://archimer.ifremer.fr/doc/00646/75831/76818.pdf |
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| Desdouits, Marion; De Graaf, Miranda; Strubbia, Sofia; Oude Munnink, Bas B.; Kroneman, Annelies; Le Guyader, Soizick; Koopmans, Marion P. G.. |
| Foodborne viral infections rank among the top 5 causes of disease, with noroviruses and hepatitis A causing the greatest burden globally. Contamination of foods by infected food handlers or through environmental pollution are the main sources of foodborne illness, with a lesser role for consumption of products from infected animals. Viral partial genomic sequencing has been used for more than two decades to track foodborne outbreaks and whole genome or metagenomics next-generation-sequencing (NGS) are new additions to the toolbox of food microbiology laboratories. We discuss developments in the field of targeted and metagenomic NGS, with an emphasis on application in food virology, the challenges and possible solutions towards future routine application |
| Tipo: Text |
Palavras-chave: Next-generation sequencing; Metagenomics; Foodborne virus; Food virology; Human enteric virus; Norovirus. |
| Ano: 2020 |
URL: https://archimer.ifremer.fr/doc/00641/75330/75988.pdf |
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