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Virology. 2015 Mar;477:1-9. doi: 10.1016/j.virol.2014.12.037. Epub 2015 Jan 17.

Next generation sequencing of the hepatitis C virus NS5B gene reveals potential novel S282 drug resistance mutations.

Author information

1
National HIV & Retrovirology Laboratories, National Microbiology Laboratory, Public Health Agency of Canada, Ottawa, Canada.
2
Department of Pathobiology, University of Guelph, Guelph, Canada.
3
Arthur Labatt Family School of Nursing, Western University, London, Canada.
4
Bioinformatics Core, National Microbiology Laboratory, Public Health Agency of Canada, Ottawa, Canada.
5
Department of Epidemiology and Community Medicine, University of Ottawa, Ottawa, Canada.
6
National HIV & Retrovirology Laboratories, National Microbiology Laboratory, Public Health Agency of Canada, Ottawa, Canada. Electronic address: james.brooks@phac-aspc.gc.ca.

Abstract

Identifying HCV drug resistance mutations (DRMs) is increasingly important as new direct acting antiviral therapies (DAA) become available. Tagged pooled pyrosequencing (TPP) was originally developed as cost-effective approach for detecting low abundance HIV DRMs. Using 127 HCV-positive samples from a Canadian injection drug user cohort, we demonstrated the suitability and efficiency of TPP for evaluating DRMs in HCV NS5B gene. At a mutation identification threshold of 1%, no nucleoside inhibitor DRMs were detected among these DAA naïve subjects. Clinical NS5B resistance to non-nucleoside inhibitors and interferon/ribavirin was predicted to be low within this cohort. S282T mutation, the primary mutation selected by sofosbuvir in vitro, was not identified while S282G/C/R variants were detected in 9 subjects. Further characterization on these new S282 variants using in silico molecular modeling implied their potential association with resistance. Combining TPP with in silico analysis detects NS5B polymorphisms that may explain differences in treatment outcomes.

KEYWORDS:

Drug resistance mutation; HCV; In silico molecular modeling; NS5B; Pyrosequencing

PMID:
25600207
DOI:
10.1016/j.virol.2014.12.037
[Indexed for MEDLINE]
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