Hepatitis C virus genetic variation and response to therapy

Two projects addressing the role of hepatitis C virus (HCV) genetic variability on response to therapy with interferon and ribavirin were conducted. The first study analyzed global effects. The second study focused on potential interactions of ribavirin with the RNA polymerase.;Pegylated-interferon plus ribavirin therapy for HCV fails in half of genotype 1 patients. Failure occurs either by true nonresponse or relapse. To determine if viral genetic differences contribute to the difference between phenotypes, we examined genetic diversity and evolution in the full open-reading frame of HCV genotype 1a consensus sequences. Pre- and post-therapy sequences of 10 nonresponders and 10 relapsers from the Virahep-C study were analyzed. Pre-therapy diversity among relapsers was higher than nonresponders in NS2. Similar numbers of mutations occurred in both phenotypes. However, mutations in NS2 of relapsers were less conservative than in nonresponders. The number and distribution of regions under positive selection was similar, although nonresponders had more foci in E2. HCV sequences were unexpectedly stable during failed therapy, both phenotypes were under selective pressure, and variation in NS2 may have contributed to the difference in response. These data support a role for viral genetic variability in determining response to therapy.;To determine if ribavirin acts in part through the HCV polymerase, 13 patients infected with HCV genotype 1b who failed interferon monotherapy and subsequently underwent interferon plus ribavirin therapy were identified: seven sustained responders and six nonresponders. The consensus sequence encoding the polymerase was determined for each patient. Amino acid variations unique to responders or nonresponders clustered asymmetrically on the polymerase surrounding the RNA-binding channel. Responders had more variations than nonresponders, and they were less conservative. Recombinant polymerases representative of patient sequences had variable activity on native and homopolymeric templates, and polymerases from two responders showed elevated incorporation of GTP relative to UTP. Because response to the second round of therapy was primarily due to ribavirin and ribavirin is a guanosine analog, these data imply that variation in the polymerase may alter interactions with ribavirin, supporting the hypothesis that ribavirin acts against HCV in humans in part through the polymerase.