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Characterization of hepatitis C virus resistance to grazoprevir reveals complex patterns of mutations following on-treatment breakthrough that are not observed at relapse

Authors Bonsall D, Black S, Howe AYM, Chase R, Ingravallo P, Pak I, Brown A, Smith DA, Bowden R, Barnes E

Received 9 November 2017

Accepted for publication 31 January 2018

Published 8 August 2018 Volume 2018:11 Pages 1119—1135


Checked for plagiarism Yes

Review by Single-blind

Peer reviewers approved by Dr Cristina Weinberg

Peer reviewer comments 2

Editor who approved publication: Dr Joachim Wink

David Bonsall,1 Stuart Black,2 Anita YM Howe,2 Robert Chase,2 Paul Ingravallo,2 Irene Pak,2 Anthony Brown,1 David A Smith,1 Rory Bowden,1 Eleanor Barnes1

On behalf of the STOP HCV Consortium

1Translational Gastroenterology Unit, University of Oxford, Oxford, UK; 2Department of Infectious Diseases, Merck & Co., Inc., Kenilworth, NJ, USA

Purpose: A detailed analysis of hepatitis C virus (HCV) resistance-associated substitutions (RASs) is required to understand why people fail direct-acting antiviral therapies. This study was conducted to assess RASs in an analysis of 2 trials evaluating the second-generation NS3/4A protease inhibitor grazoprevir (GZR) in combination with peginterferon/ribavirin.
Patients and methods: From a total of 113 participants with HCV genotype 1 infection, RASs were evaluated in 25 patients who relapsed and 6 patients with on-treatment virologic breakthrough using consensus Sanger and clonal sequence analysis of NS3/NS4a genes, with in vitro testing of replicon mutants. Next-generation sequencing (NGS) was used in a subset of participants to assess minority variants and the evolution of the whole viral genome.
Results: Baseline RASs did not predict treatment failure. Relapse was most commonly associated with RASs at D168, although additional RASs (Y56, R155 and A156) were also detected, particularly in participants with on-treatment breakthrough. Treatment-emergent RASs usually reverted to wild-type (WT), suggesting these mutations were associated with a negative fitness cost (confirmed using in vitro assays). NGS was the most sensitive assay for the detection of minor variants. Significant viral sequence divergence (up to 5.9% codons) was observed across whole genomes in association with the acquisition and reversion of RASs.
Conclusion: Relapse with GZR and peginterferon/ribavirin is commonly associated with single RASs in NS3 that generally revert to WT, while breakthrough follows more complex patterns of viral resistance. NGS suggests that large diverse pools of viral quasispecies that emerge with RASs facilitate rapid viral evolution.

Keywords: next-generation sequencing, NS3/4A protease inhibitor, resistance-associated substitution, virologic failure

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