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Original article

Resistance-associated variants in HCV subtypes 1a and 1b detected by Ion Torrent sequencing platform

Karine V Gaspareto, Roberto M Ribeiro, Fernanda de Mello Malta, Michele S Gomes-Gouvêa, Nair H Muto, Camila M Romano, Maria C Mendes-Correa, Flair J Carrilho, Ester C Sabino, João R Rebello Pinho

Corresponding author name: Karine V Gaspareto
Corresponding author e-mail: karine.gaspareto@usp.br

Citation: Antiviral Therapy 2016; 21:653-660
doi: 10.3851/IMP3057

Date accepted: 20 May 2016
Date published online: 17 June 2016


Background: As a result of increased understanding of the HCV life cycle, a new generation of drugs known as direct-acting antivirals (DAAs) was developed and is constantly being improved. At baseline, HCV variants resistant to DAA therapy may pre-exist, increasing the likelihood of treatment failure. The aim of this study was to investigate the presence of resistance-associated variants (RAVs) in treatment-naive patients infected with HCV subtypes 1a and 1b.

Methods: Next-generation sequencing was used to assess the frequencies of NS3-4A, NS5A and NS5B RAVs in 100 HCV monoinfected DAA-naive patients (HCV-1a: n=51; HCV-1b: n=49).

Results: Complete HCV sequence information was obtained for most samples. RAVs were detected in the NS3-4A (T54S, V55A, Q80K and R155K), NS5A (Q30H/R, H58P and Y93C/H/N) and NS5B (A421V) regions in 10%, 22% and 8%, respectively, of patients infected with HCV subtype-1a. Among the patients infected with HCV subtype-1b, mutations in the NS3-4A (F43I, T54S, Q80H, D168E and M175L), NS5A (L28M, R30Q, L31M, Q54H, A92T and Y93H) and NS5B (L159F, C316N, A421V and S556G) regions were observed in 12%, 53% and 31% of patients, respectively.

Conclusions: High-throughput DNA sequencing allows an easier and more complete analysis of DAA RAVs, including mutations that represent only a minor variant of the whole viral population. RAVs to the three different classes of DAAs were found in our population. The characterization of their profile in the circulating virus is relevant to determine the better treatment option for infected individuals or to guide the implementation of treatment policies.


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