Clinical Significance of In Vitro Replication–Enhancing Mutations of the Hepatitis C Virus (HCV) Replicon in Patients with Chronic HCV Infection

Background. Mutations in nonstructural (NS) hepatitis C virus (HCV) proteins enhance replication in HCV-la/b replicons. The prevalence of such mutations and their clinical significance in vivo are unknown. Methods. Parts of HCV NS3 and NS4B-NS5B genes that included 31 in vitro replication-enhancing sites were sequenced for 26 patients with chronic HCV genotype 1 infection. Results. Five patients showed specific mutations within NS3 at sites enhancing replication in the replicon. Those mutations were associated with a slower decrease in HCV RNA concentration during interferon (IFN)-α-based therapy (P =.007). Neither specific nor other mutations within NS3 and NS4B-NS5B were associated with baseline HCV RNA concentrations. Within NS5A, fewer mutations in the major HCV strain (P =.001) and increased quasi-species complexity (P =.02) and diversity (P =.02) correlated with increasing baseline HCV RNA concentrations. In silico analyses of NS3 protein structures suggested that the majority of observed mutations did not lead to major conformational changes. Conclusions. Specific mutations leading to enhanced replication in the replicon system were detected in 5 of 26 patients in vivo and were not associated with baseline HCV RNA concentrations but were associated with a slower decrease in HCV RNA concentration during IFN-α-based therapy. Quasi-species heterogeneity of NS5A correlated with baseline HCV RNA concentrations.