Hepatitis C virus (HCV) shows remarkable genetic variation in both populations and individuals, in whom it circulates as quasispecies (QS). Sequence variation within an infected host has adaptive significance and reflects the modes and intensity of selection mechanisms operating on the virus. We investigated the sequence diversity of hypervariable region 1 of HCV in liver transplant recipients and correlated it with the recurrence of hepatitis. Twenty-six patients were considered during a 2-year period; all had graft reinfection, and 14 patients developed hepatitis recurrence. Cloned sequences were obtained from sera collected before or within 1 month after orthotopic liver transplantation (OLT) and at 3 and 24 months thereafter. Sequence diversity within single sera and over consecutive samples was analyzed quantitatively by matrix comparison and phylogenetic analysis. Propagation of viral QS in the graft was markedly dependent on individual factors. Viral QS in post-OLT sera were less complex and evolved slower compared with immunocompetent subjects with chronic hepatitis. Sequence variation was greater during the first 3 months post-OLT than during the remaining period. Genetic diversity within single samples was not related to hepatitis recurrence or other clinical features. Conversely, sequence diversity over consecutive samples was reduced in patients who experienced hepatitis recurrence, in particular, in those infected with genotype 1b and with an HLA-DR mismatched graft. Selection of viral sequences was markedly impaired in liver transplant recipients and tended to be greater early after OLT. H epatitis C virus (HCV) shows high genetic diversity both in populations and within infected individuals, in whom it exists as a complex mixture of related molecular species known as viral quasispecies (QS). 1 The highly heterogeneous nature of viral populations has a central role in the mechanisms of the transmission, persistence, and pathogenesis of HCV infection. 2 The QS structure of the viral genome allows an extraordinary plasticity and an ability to adapt to variable environmental conditions and escape the host's immune surveillance. Thus, in most subjects, the immune system is unable to eradicate the infection and provide durable protection from reinfection despite persistent B-and T-cell reactivity. 3 This inefficient antiviral response is paralleled by a continuous turnover of viral variants that results from adaptation of the virus to different selective forces, rather than a progressive genetic drift. 4 Small selective advantages have greater effects on genetic compositions of viruses than major differences in spontaneous mutation rates. 5 We previously showed that in chronic HCV infection of immunocompetent hosts, genetic variation in hypervariable region 1 (HVR1) of the second envelope protein (E2) was adaptive in nature and directly dependent on the intensity and amplitude of anti-HVR1 antibody response. 6,7 Because levels of immune responsiveness can positively influence the outcome of infection, m...