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| Strubbia, Sofia; Schaeffer, Julien; Oude Munnink, Bas B.; Besnard, Alban; Phan, My V. T.; Nieuwenhuijse, David F.; De Graaf, Miranda; Schapendonk, Claudia M. E.; Wacrenier, Candice; Cotten, Matthew; Koopmans, Marion P. G.; Le Guyader, Soizick. |
| 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... |
| Tipo: Text |
Palavras-chave: Norovirus; Sewage; Oysters; Metagenomic sequencing; Metavirome. |
| Ano: 2019 |
URL: https://archimer.ifremer.fr/doc/00586/69765/67656.pdf |
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| Strubbia, Sofia; Phan, My V. T.; Schaeffer, Julien; Koopmans, Marion; Cotten, Matthew; Le Guyader, Soizick. |
| This study aimed to optimize a method to identify human enteric viruses in sewage and stool samples using random primed next-generation sequencing. We tested three methods, two employed virus enrichment based on the binding properties of the viral capsid using pig-mucin capture or by selecting viral RNA prior to library preparation through a capture using the SureSelect target enrichment. The third method was based on a non-specific biophysical precipitation with polyethylene glycol. Full genomes of a number of common human enteric viruses including norovirus, rotavirus, husavirus, enterovirus and astrovirus were obtained. In stool samples full norovirus genome were detected as well as partial enterovirus genome. A variety of norovirus sequences was... |
| Tipo: Text |
Palavras-chave: Human enteric viruses; Norovirus; Sewage; Metagenomic; Virome. |
| Ano: 2019 |
URL: https://archimer.ifremer.fr/doc/00512/62332/66592.pdf |
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