Characterization of Norovirus and Other Human Enteric Viruses in Sewage and Stool Samples Through Next-Generation Sequencing

Type Article
Date 2019-12
Language English
Author(s) Strubbia Sofia1, Phan My V. T.2, Schaeffer Julien1, Koopmans Marion2, Cotten Matthew2, Le Guyader Soizick1
Affiliation(s) 1 : Ifremer, Laboratoire de Microbiologie, LSEM-SG2M, BP 21105, 44311 Nantes Cedex 3, France
2 : Department of Viroscience, Erasmus MC, University Medical Center Rotterdam, Rotterdam, The Netherlands
Source Food And Environmental Virology (1867-0334) (Springer Science and Business Media LLC), 2019-12 , Vol. 11 , N. 4 , P. 400-409
DOI 10.1007/s12560-019-09402-3
WOS© Times Cited 5
Keyword(s) Human enteric viruses, Norovirus, Sewage, Metagenomic, Virome
Abstract

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 detected in sewage samples, with genogroup II being more prevalent. Interestingly, the pig-mucin capture enhanced not only the recovery of norovirus and rotavirus but also recovery of astrovirus, sapovirus and husavirus. Documenting sewage virome using these methods provides information for molecular epidemiology and may be useful in developing strategies to prevent further spread of viruses.

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Strubbia Sofia, Phan My V. T., Schaeffer Julien, Koopmans Marion, Cotten Matthew, Le Guyader Soizick (2019). Characterization of Norovirus and Other Human Enteric Viruses in Sewage and Stool Samples Through Next-Generation Sequencing. Food And Environmental Virology, 11(4), 400-409. Publisher's official version : https://doi.org/10.1007/s12560-019-09402-3 , Open Access version : https://archimer.ifremer.fr/doc/00512/62332/