Susceptibility of Treatment-Naive Hepatitis C Virus (HCV) Clinical Isolates to HCV Protease Inhibitors

Abstract

In order to assess the natural variation in susceptibility to hepatitis C virus (HCV) NS3 protease inhibitors (PIs) among untreated HCV patient samples, the susceptibilities of 39 baseline clinical isolates were determined using a transient-replication assay on a panel of HCV PIs, including two ␣-ketoamides (VX-950 and SCH-503034) and three macrocyclic inhibitors (MK-7009, ITMN-191, and TMC-435350). Some natural variation in susceptibility to all HCV PIs tested was observed among the baseline clinical isolates. The susceptibility to VX-950 correlated strongly with the susceptibility to SCH-503034. A moderate correlation was observed between the susceptibilities to ITMN-191 and MK-7009. In contrast, the phenotypic correlations between the ␣-ketoamides and macrocyclic inhibitors were significantly lower. This difference is partly attributable to reduced susceptibility of the HCV variants containing the NS3 polymorphism Q80K (existing in 47% of genotype 1a isolates) to the macrocyclic compounds but no change in the sensitivity of the same variants to the ␣-ketoamides tested. Our results suggest that the natural variation in baseline susceptibility may contribute to different degrees of antiviral response among patients in vivo, particularly at lower doses.Hepatitis C virus (HCV) is characterized by a high degree of genetic diversity because of its rapid replication rate and turnover, combined with the poor fidelity of the HCV RNA-dependent RNA polymerase (RdRp) (3, 5, 32). The nucleotide sequences among the six different genotypes (GTs) differ at 30 to 35% of nucleotide sites (25,26). Each of the six major GTs of HCV contains a series of closely related subtypes whose nucleotide sequences typically differ from each other by 20 to 25%. Furthermore, 5 to 8% sequence divergence is present between individual strains (variants) of HCV within a given subtype. A comprehensive analysis of HCV NS3 sequences from a larger number of GT-1 isolates found that amino acid polymorphisms were detected all along the protease sequence, including residues associated either with resistance to HCV protease inhibitors (PIs) (V36, I170, and D168) or with compensatory mutations (I72, T72, Q86, and I153) (1, 2, 30). However, many questions remain, including whether natural variation in the NS3 protease sequence impacts the susceptibility of HCV to PIs currently in development and whether there are any relationships among the chemotypes of the PIs and their baseline susceptibilities.Hepatitis C virus NS3/4A serine PIs have demonstrated potent antiviral activity in subjects infected with HCV GT-1 by specifically blocking NS3/4A protease-dependent HCV polyproprotein processing. Among these PIs, VX-950 (telaprevir) and SCH-503034 (boceprevir), the two most clinically advanced NS3/4A serine PIs, are both ␣-ketoamide compounds that covalently bind to the active-site serine of the protease (6,9,10,14,16,22). These drugs also have similar resistance profiles. Mutations V36A/M, T54A, R155K, and A156S in the NS3 protease gene, conferring a low level ...

Complexity and Catalytic Efficiency of Hepatitis C Virus (HCV) NS3 and NS4A Protease Quasispecies Influence Responsiveness to Treatment with Pegylated Interferon plus Ribavirin in HCV/HIV-Coinfected Patients

“…The V55A mutation confers low resistance to boceprevir (47). The Q80K mutation is associated with significantly reduced susceptibility to TMC-434350 and low-level resistance to vaniprevir and danoprevir but wild-type susceptibility to telaprevir and boceprevir (3). The other mutations associated with resistance were observed only as low-level variants, and most of them were detected in one clone per sample; only mutations Q41R and D168G were found in two clones of the same sample.…”

Resistance to Direct-Acting Antiviral Agents in Treatment of Hepatitis C Virus Infections

“…The sequence analysis for NS3 protease of genotype 1a in patients who received the simeprevir regimens detected a relevant polymorphism Q80K in 19-48% [13]. In vitro studies showed that this mutation decreases viral response to simeprevir by 10folds [13]. Less profound inhibition has been observed in other NS3 inhibitors including sovaprevir and asunaprevir.…”

“…The low genetic barrier for developing resistance in the second-generation protease inhibitors is still the major obstacle facing their activities. The sequence analysis for NS3 protease of genotype 1a in patients who received the simeprevir regimens detected a relevant polymorphism Q80K in 19-48% [13]. In vitro studies showed that this mutation decreases viral response to simeprevir by 10folds [13].…”

Hepatitis C virus resistance to new specifically-targeted antiviral therapy: A public health perspective

“…For instance, variations in NS3-V170 are present in most HCV genotype 1 isolates, and polymorphism in NS3-D168 is characteristic of HCV genotype 3 [32] . As the development of NS3/4A PIs was based in HCV genotype 1, subtype 1b, their antiviral activity with non-1b genotypes, may be not as effective, although some PIs inhibit more than one HCV genotype [22,42,[48][49][50] . Currently neither Boceprevir nor Telaprevir should be used in patients infected with HCV genotypes other than 1.…”

“…In fact, resistant variants arise from preexisting subpopulations of viral genomes already circulating in the infected individual, before therapy is started [19] . Selective drug pressure changes the balance between the different intra-individual HCV quasispecies; and resistant genomes dominate the circulating viruses in patients with treatment failure or suboptimal treatment response, as evidenced in patients treated with NS3/4 PIs [20][21][22] . Fortunately, resistant variants remain sensitive to Peg-IFN + RBV, which still makes their elimination possible with the current Peg-IFN + RBV treatment [16] .…”