Hepatitis C virus infections affect approximately 2% of the worldwide population and typically lead to persistent infection that may progress to cirrhosis and liver cancer. This proposal will utilize the chimpanzee model of HCV infection to explore the factors associated with viral clearance and chronic infection. We have previously characterized the global changes in liver gene expression in acute resolving and chronic HCV infection. In this proposal, the first specific aim will examine intrahepatic events during acute resolving and chronic infection at the cellular level using histological methods. The role of the interferon stimulated gene response in limiting viral spread in the liver will be examined, as will the role of cell death during acute and chronic infection. The second aim will directly measure the cumulative level of cell death in the liver during acute resolving and chronic HCV infection by genetic marking of hepatocytes with a recombinant lentivirus and analysis of changes in the complexity of viral-host DNA junctions over time. The third specific aim will extend our previous studies on cross genotype immunity and will explore the determinants of viral set point. Chimpanzees that have cleared HCV will be rechallenged with homologous and divergent viruses, and the protective immune response to the two challenges will be compared. These data will set the standard by which vaccines should be compared, since natural immunity is expected to exceed vaccine induced immunity. In addition, the basis of viral set point during chronic infection will be explored using superinfection with a divergent virus. Several different hypotheses are being tested with this approach with regard to the factors that control set point. The fourth specific aim will evaluate the of role viral proteins on genotype specific differences in interferon sensitivity using chimeric replicons between genotypes 1b and 3a. The studies in this proposal will further develop our understanding of the factors that regulate HCV infection in the liver and potentially lead to new therapeutic concepts.