Absence of HCV viral recombination following superinfection

We sought evidence of viral recombination in five recently hepatitis C virus (HCV) infected young injection drug users who became superinfected with a distinguishable strain of HCV. The entire open reading frame of plasma HCV genomes was reverse transcribed, polymerase chain reaction amplified in two fragments, and directly sequenced. In two cases of same subtype (1a > 1a) superinfections the initial and later strains were both sequenced and compared for evidence of recombination. In three cases of superinfection with strains of different genotype/subtype (3a > 1a, 1a > 3a, 1b > 1a), the later time point HCV genomes were sequenced and compared with representative genomes of the initial genotype/subtype. No evidence of intra- or inter-genotype/subtype recombination was detected using six different programs for detecting recombination. We conclude that the generation of viable recombinant HCV genomes able to dominate in the viral quasispecies is a rare event.