Previously, RNA transcripts of cDNA clones of hepatitis C virus (HCV) genotypes 1a (strains H77, HCV-1, and HC-TN), 1b (HC-J4, Con1, and HCV-N), and 2a (HC-J6 and JFH1) were found to be infectious in chimpanzees. However, only JFH1 was infectious in human hepatoma Huh7 cells. We performed genetic analysis of HCV genotype 3a (strain S52) and 4a (strain ED43) prototype strains and generated full-length consensus cDNA clones (pS52 and pED43). Transfection of Huh7.5 cells with RNA transcripts of these clones did not yield cells expressing HCV Core. However, intrahepatic transfection of chimpanzees resulted in robust infection with peak HCV RNA titers of ϳ5.5 log 10 international units (IU)/ml. Genomic consensus sequences recovered from serum at the times of peak viral titers were identical to the sequences of the parental plasmids. Both chimpanzees developed acute hepatitis with elevated liver enzymes and significant necroinflammatory liver changes coinciding with detection of gamma interferon-secreting, intrahepatic T cells. However, the onset and broadness of intrahepatic T-cell responses varied greatly in the two animals, with an early (week 4) multispecific response in the ED43-infected animal (3 weeks before the first evidence of viral control) and a late (week 11) response with limited breadth in the S52-infected animal (without evidence of viral control). Autologous serum neutralizing antibodies were not detected during the acute infection in either animal. Both animals became persistently infected. In conclusion, we generated fully functional infectious cDNA clones of HCV genotypes 3a and 4a. Proof of functionality of all genes might further the development of recombinant cell culture systems for these important genotypes.Hepatitis C virus (HCV) is a small, enveloped virus with a single-stranded RNA genome, approximately 9.6 kb in length. The genome consists of 5Ј and 3Ј untranslated regions (UTRs) and a single open reading frame (ORF), encoding structural proteins (Core, E1, and E2), p7, and nonstructural proteins (NS2, NS3, NS4A, NS4B, NS5A, and NS5B) (22). Due to significant genetic heterogeneity, HCV was classified into 7 major genotypes and numerous subtypes, differing Ͼ30% and Ͼ20%, respectively, at the nucleotide level and at the amino acid level. Strains/isolates differ in 2 to 10% at the nucleotide/ amino acid level, and quasispecies typically differ in up to 2% at the nucleotide/amino acid level (70). As a main cause of liver cirrhosis and hepatocellular carcinoma, chronic HCV infection poses a major public health burden. There is no vaccine available, and combination therapy with alpha interferon and ribavirin is characterized by many side effects and contraindications, as well as low efficacy (22). Research on the HCV life cycle and new therapeutics requires well-characterized experimental models and reagents representing the different virus variants.Chimpanzees, the only animal model of HCV infection mirroring immunopathogenesis and viral persistence observed in human infections (4, 80), can be ...