No correspondence between resistance mutations in the HCV-NS3 protease at baseline and early telaprevir-based triple therapy

Abstract

Direct-acting antiviral (DAA)-based therapy is the new standard treatment for chronic hepatitis C virus (HCV) infection. However, protease inhibitor (PI)-resistant viral variants have been often described. This study aimed to examine HCV-NS3 protease variants at baseline and at 4 weeks under triple therapy. To this end, we analyzed the presence of variants in HCV-NS3 protease region from peripheral blood samples of 16 patients infected with HCV-1 at baseline and at 4 weeks of combined therapy with telaprevir, pegylated interferon, and ribavirin, using next-generation sequencing. Several variants with synonymous and non-synonymous amino acid substitutions were detected at both time points. Variants detected at low frequency corresponded to 74% (HCV-1a) and 35% (HCV-1b) of non-synonymous substitutions. We found nine PI-resistance-associated variants (V36A, T54S, V55I, Q80K, Q80R, V107I, I132V, D168E, M175L) in HCV-NS3 of 10 patients. There was no correspondence of resistance-associated variant profile between baseline and at 4 weeks. Moreover, these resistance variants at baseline and short-term treatment are not good predictors of outcome under triple therapy. Our study also shows a large number of others minor and major non-synonymous variants in HCV-NS3 early in telaprevir-based therapy that can be important for further drug resistance association studies with newly developed PI agents.

Detection of Natural Resistance-Associated Substitutions by Ion Semiconductor Technology in HCV1b Positive, Direct-Acting Antiviral Agents-Naïve Patients

“…Substitution NS3 V36L—conferring resistance to BOC and possibly to telaprevir (TVR) or simeprevir (SMV) [ 5 ] or grazoprevir (GZR) [ 36 ]—was detected in a treatment-naïve patient’s (HCV17) HCV isolate. We also identified substitution NS3 I132V [ 29 ], which is associated with possible resistance to TVR, in 4 patients: HCV04, HCV06, HCV08, HCV19. The NS3 V170I GZR RAS was found in HCV isolate from patient HCV20 [ 37 ] ( Table 3 ).…”

“…In the NS3 region, we found two RASs, NS3 V36L [ 45 ] and NS3 I132V [ 29 ], in isolates from one patient and four patients, respectively. The NS3 V36L variant carried by patient HCV17 confers resistance to BOC and possibly to TVR or SMV and is reported to be present in 0.5% of all previously studied worldwide HCV1b strains [ 46 ].…”

“…The short read platforms (e.g., the Illumina ® sequencers) are currently the most widely used, but the advantages of longer read lengths in reads assembly and the preservation of mutational linkage over longer distances [ 22 , 23 , 24 ] ensure a place for longer read technologies, such as the Ion Torrent platforms for virus sequencing. As a case in point, the Ion Personal Genome Machine (PGM) Sequencer (Life Technologies, Carlsbad, CA, USA) has recently been used to detect low-level drug resistance variants in HCV and HIV quasispecies [ 25 , 26 , 27 , 28 , 29 ].…”

Resistance-Associated Variants in HCV Subtypes 1a and 1b Detected by Ion Torrent Sequencing Platform

“…To our knowledge, this is the first published study showing the use of this technology for the full length HCV coding region. A previous study carried out in Brazil analysed only the NS3 region of 16 patients (8 subtype-1a and 8 subtype-1b) before initiating triple therapy and after 4 weeks of treatment (TVR plus PR) using the Ion Torrent technology [27].…”

Resistance mutations of NS3 and NS5b in treatment-naïve patients infected with hepatitis C virus in Santa Catarina and Rio Grande do Sul states, Brazil

“…The primary targets of DAAs are nonstructural proteins essentials for HCV replication, which include the NS3 protease, NS5B polymerase, and NS5A protein (Paolucci et al, 2013;Lontok et al, 2015). However, a challenge in HCV treatment is the emergence of viral resistance mutations that reduces susceptibility of the virus to DAA therapies (Hoffmann et al, 2015;Gededzha et al, 2017). The development of resistance-associated variants (RAVs) is due to the high level of virus variability, from the combination of the virus' high replication rate, low RNA polymerase fidelity rate, and selective pressure for drug or immunomediated treatment (Peres-da-Silva et al, 2012;Paolucci et al, 2013;Gededzha et al, 2017).…”