Genetic heterogeneity of hypervariable region 1 of the hepatitis C virus (HCV) genome and sensitivity of HCV to alpha interferon therapy

Hepatitis C virus (HCV) populations persist in vivo as a mixture of heterog eneous viruses called quasispecies. The relationship between the genetic he terogeneity of these variants and their responses to antiviral treatment re mains to be elucidated. We have studied 26 virus strains to determine the i nfluence of hypervariable region 1 (HVR-1) of the HCV genome on the effecti veness of alpha interferon (IFN-alpha) therapy. Following PCR amplification , we cloned and sequenced HVR-1, Pretreatment serum samples from 13 individ uals with chronic hepatitis C whose virus was subsequently eradicated by tr eatment were compared with samples from 13 nonresponders matched according to the major factors known to influence the response, i.e., sex, genotype, and pretreatment serum HCV RNA concentration. The degree of virus variation was assessed by analyzing 20 clones per sample and by calculating nucleoti de sequence entropy (complexity) and genetic distances (diversity), Types o f mutational changes were also determined by calculating nonsynonymous subs titutions per nonsynonymous site (K-a) and synonymous substitutions per syn onymous site (K-s). The paired-comparison analysis of the nucleotide sequen ce entropy and genetic distance showed no statistical differences between r esponders and nonresponders. By contrast, nonsynonymous substitutions were more frequent than synonymous substitutions (P less than or equal to 0.05) in responders, but there was no significant difference in nonresponders. No nsynonymous substitutions tended to be more frequent than synonymous substi tutions in women (P = 0.06) but not in men, Nucleotide entropy and genetic distances were significantly related to serum RNA concentration (P less tha n or equal to 0.01), Our findings suggest that after controlling for the ma jor determinants of interferon response, neither complexity nor diversity o f the HVR-1 region is associated per se with virus eradication. Because a h igher proportion of nonsynonymous substitutions than synonymous substitutio ns was found only in responders, host anti-HCV-specific immune response rat her than viral factors may be playing an important role in the interferon r esponse.