HCV-1b intra-subtype variability: Impact on genetic barrier to protease inhibitors

Abstract

a b s t r a c tDue to error-prone RNA polymerase and the lack of proofreading mechanisms, to the spread worldwide and probable long-term presence in human population, HCV showed a high degree of inter-and intrasubtype genetic variability.Protease inhibitors (PIs), a new class of drugs, have been designed specifically on the HCV genotype 1 NS3 protease three-dimensional structure. The viral genetic barrier limits the efficacy of PIs, and fourteen loci in the HCV NS3 gene are involved in resistance to PIs. A sensitive method (15 UI/ml) for study the HCV genetic profile of 125 strains from patients naïve to PIs, was developed through the use of new degenerate primers for subtype 1b.We observed the presence of naturally resistance-associated variants in 14% of the HCV strains (V36L, F43S, T54S, I153V, R155Q, D168A/G). T54S was the most common mutation (4%) detected.We investigated, through minimal score (m.s.) calculating, how the HCV intra-subtype 1b variability modifies the genetic barrier to PIs. For >60% of strains a single transition (m.s. of 1) was required for selection of low to medium resistance mutations, while more than one transition/transversion (m.s. P2.5) or one transition plus one transversion (m.s. P3.5) was necessary for most of the high level PI-resistantassociated mutations, except for A156V, for which a single transition was sufficient (m.s. of 1). However, the presence at locus 36 of the amino acid polymorphism S36 in one case and the wild type V36 in 6 isolates, encoded by unusual GTA or GTG codons, might determined a higher probability of V36L/M mutations because of the reduction of the genetic barrier. Instead, the presence of the CGA and CGT codons in the 155 th position increases the genetic barrier for R155M or R155Q/M.The large intra-subtype variability, suggests that a routine baseline resistance test must be used before PIs-treatment.

Significance of mutations in the region coding for NS3/4 protease in patients infected with HCV genotype 1b.

“…Mutations I71 and T72 are compensatory for mutations V55 and M175, and compensatory mutation Q86 is present in the case of mutation at position Q80. 15 In our research, compensatory mutation T72 was observed in 1 patient in relation to substitution at position T54. Also, mutation Q86 was detected in a single patient, who also had a mutation at Q80.…”

“…Ferraro et al detected such mutations in 14% patients infected with HCV genotype 1b at positions V36, F43, T54, I153, R1 55, and D168. 15 In similar studies, Paolucci et al, on the basis of a group of 39 treatment-naïve people infected with HCV genotype 1b, demonstrated the presence of mutations at positions V55, Q80 and M175 in 10% of the patients. 11 In the context of antiviral therapy, mutations decreasing the efficacy of boceprevir and telaprevir are most often detected, which, considering the frequent adverse reactions of these agents, justifies the recommendation to avoid their use in the treatment.…”

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

“…Non-synonymous resistance variants were detected at baseline in the peripheral blood of all patients, supporting the existence of circulating viral populations. The improved detection capacity of the NGS method used here may explain the observation of more highly prevalent and variable mutations at baseline in the peripheral blood than those detected by previous studies in Brazil [11] , [15] , [24] , [25] and other countries [12] , [18] , [26] , [27] . Our results therefore confirm and expand previous research, providing a comprehensive databank of non-synonymous HCV-NS3 variants induced by short-term therapy, which can be of potential importance for future drug resistance association studies involving approved and newly developed PI agents.…”

“…The predictive potential of baseline resistance variants remains controversial. Some authors still support routine baseline resistance mutation detection before PI therapy [18] , while others report that resistant variants emerging during PI therapy are the same as those identified at baseline [19] , [20] . However, most studies have investigated emerging resistance mutations late in treatment or post-treatment, i.e., at the time of viral load re-elevation [19] .…”

“…Even though routine baseline resistance mutation detection before PI therapy is still prescribed as a prognostic tool [18] , the predictive value of these mutations at baseline remains controversial. In fact, recent research [19] , [20] has suggested that resistant variants that emerge during PI therapy might not be the same as those identified at baseline.…”