Evolution of the Hepatitis C Virus Second Envelope Protein Hypervariable Region in Chronically Infected Patients Receiving Alpha Interferon Therapy

Abstract

Sustained hepatitis C virus (HCV) RNA clearance is achieved in 8 to 12% of patients with chronic HCV infection treated with alpha interferon (IFN-α) at the approved dose of 3 MU three times a week for 6 months and in about 25% of those receiving this treatment for 12 months. We used single-strand conformation polymorphism analysis combined with cloning and sequencing strategies to characterize the genetic evolution of HCV second envelope gene hypervariable region 1 (HVR1) quasispecies during and after IFN therapy in patients who failed to clear HCV RNA. Sustained HCV RNA clearance was achieved in 6% of patients. Profound changes in HVR1 quasispecies major variants were estimated to occur in 70% of the patients during and after therapy. These changes were evolutionary and were characterized by shifts in the virus population, related to selection and subsequent diversification of minor pretreatment variants. The quasispecies changes appeared to be induced by changes in the host environment likely resulting from the IFN-induced enhancement and post-IFN attenuation of neutralizing and possibly cytotoxic responses against HVR1. The remaining patients had no apparent changes in HVR1 quasispecies major variants, suggesting selection of major pretreatment variants, but some changes were observed in other genomic regions. We conclude that IFN-α administration and withdrawal profoundly alters the nature of circulating HCV quasispecies, owing to profound changes in virus-host interactions, in patients in whom sustained HCV RNA clearance fails to occur. These changes are associated with profound alterations of the natural outcome of HCV-related liver disease, raising the hypothesis of a causal relationship.

Hepatitis C Virus Resistance to Antiviral Therapy

“…Nonresponders or partial responders and, more often, responder-relapsers to a first course of IFN-␣ may achieve a sustained virologic response after a second identical course of IFN-␣ therapy. 79,81,82 In such cases, we observed significant qualitative HCV quasispecies changes after the first course of IFN. 79 The selected HCV variants were not intrinsically resistant to IFN-␣, because they were definitively cleared after the second course of IFN.…”

“…79,81,82 In such cases, we observed significant qualitative HCV quasispecies changes after the first course of IFN. 79 The selected HCV variants were not intrinsically resistant to IFN-␣, because they were definitively cleared after the second course of IFN. They just became fit in the environment created by the administration and subsequent withdrawal of IFN during and after the first course of treatment.…”

“…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:…”

“…They became nonfit and could be cleared during the second course of IFN because the nature of the host-virus interaction was different several months after the first course and could be tipped toward sustained viral clearance by IFN at that time. 79 Viral factors, nevertheless, appear to play an important role in HCV resistance to IFN-based therapy, probably conferring HCV quasispecies and infected cell properties that allow them to survive in the context of IFN administration. High quasispecies genetic complexity (i.e., a large size of the quasispecies sequence repertoire) at the beginning of therapy is an independent predictor of treatment failure.…”

“…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.…”