h Chronic hepatitis C virus (HCV) infection can lead to liver cirrhosis in up to 20% of individuals, often requiring liver transplantation. Although the new liver is known to be rapidly reinfected, the dynamics and source of the reinfecting virus(es) are unclear, resulting in some confusion concerning the relationship between clinical outcome and viral characteristics. To clarify the dynamics of liver reinfection, longitudinal serum viral samples from 10 transplant patients were studied. Part of the E1/E2 region was sequenced, and advanced phylogenetic analysis methods were used in a multiparameter analysis to determine the history and ancestry of reinfecting lineages. Our results demonstrated the complexity of HCV evolutionary dynamics after liver transplantation, in which a large diverse population of viruses is transmitted and maintained for months to years. As many as 30 independent lineages in a single patient were found to reinfect the new liver. Several later posttransplant lineages were more closely related to older pretransplant viruses than to viruses detected immediately after transplantation. Although our data are consistent with a number of interpretations, the persistence of high viral genetic variation over long periods of time requires an active mechanism. We discuss possible scenarios, including frequency-dependent selection or variation in selective pressure among viral subpopulations, i.e., the population structure. The latter hypothesis, if correct, could have relevance to the success of newer direct-acting antiviral therapies.T he hepatitis C virus (HCV; family Flaviviridae, genus Hepacivirus) infects more than 180 million people worldwide and is a leading global cause of liver disease and cancer (3, 26). Since individuals can remain asymptomatic for decades, the true prevalence is potentially much greater than current estimates of ϳ3% of the world population (50). At present, no vaccine is available, and pharmacological treatment is only moderately successful, particularly for the most prevalent subtypes circulating in the United States and Europe (3), due in part to a prolonged asymptomatic phase of chronic infection that hinders early identification of HCV transmission among individuals. Although the use of direct-acting antiviral drugs (including two recently licensed protease inhibitors) offer improved sustained antiviral response rates (29), drug treatments will not be successful in all patients (47), and antiviral resistance is likely to play a significant role in treatment failure (21). Thus, chronic HCV infection remains a major public health concern.Liver cirrhosis develops in up to 20% of HCV-infected individuals, who will eventually require a liver transplant (3). However, the new liver is infected within minutes following transplant (16), serum viral load increases 10-to 20-fold relative to pretransplant levels (12), and the clinical course of disease is accelerated (11). Characteristics of the infecting virus and its anatomical source(s) are unknown, reflecting the lack of a pr...