Frequency distribution of HCV resistance-associated variants in infected patients treated with direct-acting antivirals

Bianca Catarina Azeredo Cabral,Juliene Antonio Ramos,Amanda Laryssa De Melo Silveira,Érica Ramos Dos Santos Nascimento,Selma Baía Ferreira,Henrique Sérgio Moraes Coelho,Rodrigo Soares Moura-Neto,Cristiane Alves Villela-Nogueira,Luísa Hoffmann,Rosane Silva

doi:10.1016/j.ijid.2021.12.320

Abstract

Hepatitis C virus (HCV) is a global public health problem. Second-generation direct-acting antivirals targeting non-structural regions on the viral genome are the cornerstone for treatment of chronic infection. However, resistance-associated variants (RAVs) have been reported to be associated with therapeutic failure. The aim of this study was to assess the frequency of variants, including RAVs, in the NS3, NS5A and NS5B regions at baseline in Brazilian patients with chronic hepatitis C with HCV genotypes 1a, 1b and 3a. Serum samples from 13 patients were used to obtain viral RNA. Massively parallel sequencing was performed using genotype-specific amplicons and a panel of Ampliseq technology for all genotypes. Several non-synonymous substitutions were detected at baseline for 11 responders and pre-/post-treatment for two non-responders. HCV genotype 3a was found to have significantly more non-synonymous substitutions than HCV genotype 1 in the NS3 and NS5A regions. Analyses were conducted using quantitative and qualitative inter- and intrapatient comparisons. Variants that confer resistance to the treatment used by the patients were found in both responders and non-responders. A wide frequency distribution of RAVs was found at baseline, and this did not interfere with the achievement of a sustained response. Evaluation of the presence of RAVs requires additional study in order to determine clinical relevance.

Highlights

Hepatitis C virus (HCV) is a global public health problem that causes severe liver disease with important comorbidity and mortality, with approximately 71 million people infected (World Health Organization, 2020)
The aim of this study was to assess the frequency of amino acid substitutions, including resistance-associated variants (RAVs), in the NS3, NS5A and NS5B regions at baseline in patients with chronic hepatitis C infected with HCV genotypes 1a, 1b and 3a using massively parallel sequencing
The NS3, NS5A and NS5B regions generated a total of 1,003,938 reads (Table S1, see online supplementary material)

Summary

Introduction

Hepatitis C virus (HCV) is a global public health problem that causes severe liver disease with important comorbidity and mortality, with approximately 71 million people infected (World Health Organization, 2020). The aim of this study was to assess the frequency of amino acid substitutions, including RAVs, in the NS3, NS5A and NS5B regions at baseline in patients with chronic hepatitis C infected with HCV genotypes 1a, 1b and 3a using massively parallel sequencing. It provides comprehensive information on non-synonymous substitutions, even at low frequencies, detected at baseline, and explores the prognostic value of RAVs in order to determine clinical relevance. Evaluation of the presence of RAVs requires additional study in order to determine clinical relevance

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Discussion

Conclusion