Evolution of Hepatitis C Virus Quasispecies in Hypervariable Region 1 and the Putative Interferon Sensitivity-Determining Region during Interferon Therapy and Natural Infection

Abstract

To study hepatitis C virus (HCV) genetic mutation during interferon (IFN) therapy, the temporal changes in HCV quasispecies heterogeneity were compared before and after treatment for nine patients infected with HCV genotype 1, including four nonresponders, four responders who relapsed after therapy, and one responder who experienced a breakthrough of viremia during therapy. Nine untreated patients with an average time between specimens of 8.4 years served as controls. Sequences from the second envelope glycoprotein gene hypervariable region 1 (HVR1) and the putative IFN sensitivity-determining region (ISDR) of the nonstructural NS5A gene were analyzed by heteroduplex mobility assays and nucleotide sequencing. A strong positive correlation was found between the percent change in a heteroduplex mobility ratio (HMR) and percent change in nucleotide sequence (r = 0.941,P < 0.001). The rate of fixation of mutations in the HVR1 was significantly higher for IFN-treated patients than for controls (6.97 versus 1.31% change in HMR/year; P = 0.02). Similarly, a higher rate of fixation of mutations was observed in the ISDR for IFN-treated patients than for untreated controls, although the result was not significant (1.45 versus 0.15 amino acid changes/year; P = 0.12). On an individual patient basis, IFN therapy was associated with measurable HVR1 and ISDR mutation in nine of nine (100%) and two of nine (22.2%) patients, respectively. Evolution to IFN-resistant ISDR sequences was observed in only one of nine IFN-treated patients. These data suggest that IFN therapy frequently exerts pressure on the HCV envelope region, while pressure on the ISDR was evident in only a subset of patients. Thus, the selection pressures evoked on HCV genotype 1 quasispecies during IFN therapy appear to differ among different patients.

High amino acid variability within the NS5A of hepatitis C virus (HCV) is associated with hepatocellular carcinoma in patients with HCV-1b–related cirrhosis

“…These residues have been described as quite heterogeneous among different HCV-1b isolates. 16,20,39,49,50 On the other hand, serine residues, that are probably implicated in the hyperphosphorylation of NS5A 61,62 were highly conserved in the majority of viral isolates analyzed in this study.…”

“…15,16,[34][35][36][37][38] ‡According to references. [39][40][41][42][43][44][45][46][47][48][49][50][51][52][53][54] found between patients with and without HCC. When compared with the deduced consensus sequence derived from all sequenced isolates, 3 or more aa changes within the PKR-bd were observed in 60% of patients with HCC, but only in 6% of those without evidence of tumor.…”

“…Although emergence of variants with mutated NS5A under interferon pressure has been reported, 35,36,39,41,47,50 NS5A appears to be a relatively stable region of the HCV genome in the absence of therapy. 63 Stability over time of the NS5A was also observed in the present study.…”

Hepatitis C Virus Resistance to Antiviral Therapy

“…In the vast majority of, if not all, patients who do not achieve a sustained virologic response, IFN administration and subsequent IFN withdrawal are associated with significant qualitative changes in the composition of HCV quasispecies. [76][77][78][79][80] Both the mechanisms of action of IFN-␣ and recent clinical and virologic observations suggest that the selected HCV quasispecies variants are not intrinsically resistant to IFN-␣ but just become fit in the environment created by IFN-induction of host responses. This is supported by the following arguments:…”

“…Failure to clear HCV RNA during therapy is associated with significant qualitative HCV quasispecies changes in most, if not all, cases. [76][77][78][79][80] Although viral escape could be one of the mechanisms involved in treatment failure, most of these changes appear to be the consequence of the inability of the host to clear infection. They result in the accumulation of mutations on HCV genome during ongoing replication and selection of the corresponding variants.…”