Characterization of Norovirus and other human enteric viruses in sewage and stool samples through next-generation sequencing

Strubbia, S., Phan, M. V.T., Schaeffer, J., Koopmans, M., Cotten, M. and Le Guyader, F. S. (2019) Characterization of Norovirus and other human enteric viruses in sewage and stool samples through next-generation sequencing. Food and Environmental Virology, 11(4), pp. 400-409. (doi: 10.1007/s12560-019-09402-3) (PMID:31446609) (PMCID:PMC6848244)

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.

• Item Type: Articles
• Additional Information: This work was funded by EU-H2020 Grant No. 643476 COMPARE. My V.T. Phan is supported by Marie Sklodowska-Curie Individual Fellowship, funded by European Union’s Horizon 2020 research and innovation programme (Grant Agreement No. 799417).
• Status: Published
• Refereed: Yes
• Glasgow Author(s) Enlighten ID: Cotten, Professor Matthew
• Authors: Strubbia, S., Phan, M. V.T., Schaeffer, J., Koopmans, M., Cotten, M., and Le Guyader, F. S.
• College/School: College of Medical Veterinary and Life Sciences > School of Infection & Immunity; College of Medical Veterinary and Life Sciences > School of Infection & Immunity > Centre for Virus Research
• Journal Name: Food and Environmental Virology
• Publisher: Springer
• ISSN: 1867-0334
• ISSN (Online): 1867-0342
• Published Online: 24 August 2019
• Copyright Holders: Copyright © 2019 The Authors
• First Published: First published in Food and Environmental Virology 11:400-409
• Publisher Policy: Reproduced under a Creative Commons License