The purpose of this R21 application is to study HCV recombination, or the exchange of genetic material resulting in hybrid genomes. For HIV-1, recombination was obscure until 1994 but is now recognized as a major mode of genetic diversification, representing an important mechanism for immune evasion and drug resistance. Recently, the first evidence of recombination in HCV was reported in specimens from St. Petersburg, Russia. To date, no other recombinant HCV genomes have been described. Because most studies of HCV genetic sequence have involved small amplicons, whereas identification of a recombinant strain requires examination of multiple genomic regions, we hypothesize that HCV recombination is a more common phenomenon than currently appreciated, and propose initial studies of its frequency and character. We have assembled a large repository of specimens for which genotype has been determined at by sequence analysis of the E1 gene. These specimens have been obtained from infected individuals in 4 U.S. cities where genotypes 1, 2, and 3 predominate, as well as Thailand where genotypes 1, 3, and 6 predominate. We also describe initial investigations of a mixed infection, containing two distinct populations of HCV, which suggest the presence of recombination. Building on years of experience investigating HIV-1 recombination, HCV sequence variation, and the genetic epidemiology of diverse HCV subtypes in Egypt, we propose to examine our repository for evidence of recombination in HCV. The goal of this application is to determine whether genetic recombinant HCV is prevalent, and to performed detailed analysis of recombinant genomes. Specifically, we aim to: (1) identify specimens with discordant genotypes at separate HCV loci, (2) examine specimens containing more than one strain to detect incident recombination, and (3) characterize putative recombinant genomes in detail. Our repository includes well-characterized longitudinally- acquired specimens and we are applying methods for which we have established expertise; therefore, this application has a high likelihood of success. Because the impact of HCV recombination has not yet been determined, R21 funding will provide adequate preliminary data to establish the importance and proper conduct of more extensive investigations. ? ? ?
