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Metagenomic to evaluate norovirus genomic diversity in oysters: Impact on hexamer selection and targeted capture-based enrichment ArchiMer
Strubbia, Sofia; Schaeffer, Julien; Besnard, Alban; Wacrenier, Candice; Le Mennec, Cecile; Garry, Pascal; Desdouits, Marion; Le Guyader, Soizick.
Human virus transmission through food consumption has been identified since many years and the international trade increases the risk of dissemination of viral pathogens. The development of metagenomic approach holds many promises for the surveillance of viruses in food and water. This work aimed to analyze norovirus diversity and to evaluate strain-dependent accumulation patterns in three oyster types by using a metagenomic approach. Different hexamer sets to prime cDNA were evaluated before capture-based approach to enhance virus reads recovery during deep sequencing. The study includes the use of technical replicates of artificially contaminated oysters and the analysis of multiple negatives controls. Results showed a clear impact of the hexamer set...
Tipo: Text Palavras-chave: Norovirus; Oysters; Metagenomic; Human enteric viruses..
Ano: 2020 URL: https://archimer.ifremer.fr/doc/00614/72575/71535.pdf
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