Background
HIV immune escape follows a predictable mutational path in response to the HLA alleles carried by an individual. The kinetics of CTL epitope escape and reversion in subtype B HIV-1 infected individuals have recently been reported, however, the inferences drawn from them were limited by the absence of information about the transmitted sequence. To address these issues, we examined Gag, Pol and Nef sequences in both partners of 148 epidemiologically-linked transmission pairs from an African subtype C cohort.