Polymorphisms and resistance mutations of hepatitis C virus on sequences in the European hepatitis C virus database

Abstract

AIMTo evaluate the occurrence of resistant mutations in treatment-naïve hepatitis C virus (HCV) sequences deposited in the European hepatitis C virus database (euHCVdb).METHODSThe sequences were downloaded from the euHCVdb (). The search was performed for full-length NS3 protease, NS5A and NS5B polymerase sequences of HCV, separated by genotypes 1a, 1b, 2a, 2b and 3a, and resulted in 798 NS3, 708 NS5A and 535 NS5B sequences from HCV genotypes 1a, 1b, 2a, 2b and 3a, after the exclusion of sequences containing errors and/or gaps or incomplete sequences, and sequences from patients previously treated with direct antiviral agents (DAA). The sequence alignment was performed with MEGA 6.06 MAC and the resulting protein sequences were then analyzed using the BioEdit 7.2.5. for mutations associated with resistance. Only positions that have been described as being associated with failure in treatment in in vivo studies, and/or as conferring a more than 2-fold change in replication in comparison to the wildtype reference strain in in vitro phenotypic assays were included in the analysis.RESULTSThe Q80K variant in the NS3 gene was the most prevalent mutation, being found in 44.66% of subtype 1a and 0.25% of subtype 1b. Other frequent mutations observed in more than 2% of the NS3 sequences were: I170V (3.21%) in genotype 1a, and Y56F (15.93%), V132I (23.28%) and I170V (65.20%) in genotype 1b. For the NS5A, 2.21% of the genotype 1a sequences have the P58S mutation, 5.95% of genotype 1b sequences have the R30Q mutation, 15.79% of subtypes 2a sequences have the Q30R mutation, 23.08% of subtype 2b sequences have a L31M mutation, and in subtype 3a sequences, 23.08% have the M31L resistant variants. For the NS5B, the V321L RAV was identified in 0.60% of genotype 1a and in 0.32% of genotype 1b sequences, and the N142T variant was observed in 0.32% of subtype 1b sequences. The C316Y, S556G, D559N RAV were identified in 0.33%, 7.82% and 0.32% of genotype 1b sequences, respectively, and were not observed in other genotypes.CONCLUSIONHCV mutants resistant to DAAs are found in low frequency, nevertheless they could be selected and therapy could fail due resistance substitutions in HCV genome.

Evolution of Resistance-Associated Variants of All-Oral Direct-Acting Antiviral Therapy of Hepatitis C in a Clinical Setting

“…In line with published data on the association between RAVs for different DAA and HCV genotype/subtype, this study indicated that subtype 1a and 1b presented RAVs especially for SMV and DSV, respectively, while RAVs for DCV, LDV and DSV were more represented in genotypes 3 and 4 [22,25].…”

“…In agreement with data on sequences from the European cohorts, NS5B RAVs were detected more frequently in subtype 1b (60%) compared to subtype 1a and genotype 4 (42%-32.5% and 25%, respectively) [31,25]. The substitution S556G, that confers intermediate resistance to DSV, appeared at a higher frequency in subtype 1b than in subtype 1a (56% vs. 28%).…”

“…Interestingly, 33% of these subjects had been previously treated with TPV or SMV [22,27,25]. These data are in line with a recent work showing a higher genetic barrier to resistance for most protease inhibitors of HCV subtype 1b compared with subtype 1a [11].…”

“…#75 1a pegINF+TPV+RBV LDV+SOF+RBV NA -#77 1a pegINF+TPV+RBV LDV+SOF+RBV T54S, V55I, S122G T54S, V55I, S122G, R155K #84 1a pegINF+TPV+RBV SOF+DAC i Q80K T54S, Q80K, R155K #92 1a pegINF+TPV+RBV SOF+DAC -R155K #99 1a pegINF+TPV+RBV LDV+SOF+RBV S122G S122G, R155K #111 1a pegINF+TPV+RBV LDV+SOF+RBV -V36M, R155K #14 1b pegINF+TPV+RBV SOF+DAC+RBV NA Q41R, V55A, S122A, M175L #56 1b pegINF+TPV+RBV LDV+SOF+RBV NA -#79 4d pegINF+SMV+RBV The current report highlighted that the overall pre-treatment prevalence of DAA RAVs was high (more than 60%) in all the target regions using either 1% or 15% cut-off, being near 35% in NS3 and NS5B regions. This frequency is higher than that previously reported, particularly for the proportion of RAVs in NS5B region, that in this study was found similar to that observed in NS5A [5,9,22,24,25]. This discrepancy might in part depend on the different sensitivity of the sequencing method used; indeed, most of published studies used a direct sequencing with sensitivity around 20% rather than the NSG approach with a cut-off of 1%-15% used in the present investigation.…”

Research progress on the direct antiviral drugs for hepatitis C virus

“…A naturally high rate of genetic mutation due to low fidelity of RNA replication generates genetic diversity of HCV (18). Based on genetic differences between HCV isolates, the HCV species is classified into six genotypes (1-6) with several subtypes within each genotype.…”