Six donor-recipient clusters of hepatitis C virus (HCV)-infected individuals were studied. For five clusters the period of infection of the donor could be estimated, and for all six clusters the time of infection of the recipients from the donor via blood transfusion was also precisely known. Detailed phylogenetic analyses were carried out to investigate the genomic evolution of the viral quasispecies within infected individuals in each cluster. The molecular clock analysis showed that HCV quasispecies within a patient are evolving at the same rate and that donors that have been infected for longer time tend to have a lower evolutionary rate. Phylogenetic analysis based on the split decomposition method revealed different evolutionary patterns in different donor-recipient clusters. Reactivity of antibody against the first hypervariable region (HVR1) of HCV in donor and recipient sera was evaluated and correlated to the calculated evolutionary rate. Results indicate that anti-HVR1 reactivity was related more to the overall level of humoral immune response of the host than to the HVR1 sequence itself, suggesting that the particular sequence of the HVR1 peptides is not the determinant of reactivity. Moreover, no correlation was found between the evolutionary rate or the heterogeneity of the viral quasispecies in the patients and the strength of the immune response to HVR1 epitopes. Rather, the results seem to imply that genetic drift is less dependent on immune pressure than on the rate of evolution and that the genetic drift of HCV is independent of the host immune pressure.Hepatitis C virus (HCV) causes persistent infection in a majority of infected individuals. Among the possible mechanisms explaining persistence are the relatively poor immunogenicity of the virus, particularly of the envelope glycoproteins; the low level of viremia outside the preseroconversion period; and the considerable variability of the viral genome, leading to substantial changes in the viral epitopes over time in the same individual (22,36). One of the main contributors to these genomic changes is the hypervariable region 1 (HVR1) located at the N terminus of the major envelope glycoprotein E2. Mutations in HVR1, which is critical for virus interaction with target cells (34, 48), produce escape mutants, a likely contributing factor to viral persistence (24,38,46).The host of HCV, primate or human, seems in most cases unable to generate an effective immune response, whether humoral, as levels of antibody to the E2 protein or HVR1 are typically low or undetectable, or cellular, as no evidence of a specific T-cell response to E2 epitopes has been provided (3,16,17,37). This feature was supported by data collected in vivo indicating that neither natural defenses nor passive immunotherapy was able to prevent reinfection of a chronically infected patient or animal with the same or related viruses (7,30).Some studies of HCV evolution over time, in the same infected individual or in different individuals infected with the same viral quasispecies...