HIV-1 evolution in recently infected patients

HIV diversity and evolution in-vivo may contribute to viral persistence, disease pathogenesis, and evolution of drug resistance. Studies aimed at understanding diversity and population genetics in acute and early HIV infection are fundamental to the development of vaccine strategies. Viral diversity is influenced by many factors including immune selection. However, there are conflicting data on the transmission and reversion of epitope-associated mutations in HIV-infected patients. The goal of this study is to characterize population structure and diversity in early HIV infection in-vivo and to identify evolutionary patterns over the first months and years after seroconversion. A limiting-dilution PCR-based assay, called the single genome sequencing assay (SGS), was designed to allow one to obtain multiple individual viral sequences from HIV-infected patients in order to examine viral population genetics in-vivo. Longitudinal plasma samples from acute or recent infection that spanned up to 5 years post-seroconversion were obtained from 14 HIV-1, subtype B-infected patients. Approximately 20 single genome sequences were obtained from gag-pro-pol and env for each sample. The first available sample after infection in 12 patients revealed HIV-1 populations with low genetic diversity, consistent with the transmission of a single viral variant. Two patients showed high diversity and complex population structures in samples collected only days after seroconversion, consistent with infection resulting from transmission of multiple HIV-1 variants. Distinct patterns of evolution were seen between single and multiple variant infected patients, however, samples from all patients differed in protease (PR) and reverse transcriptase (RT) from the consensus B sequence by mutations confined to epitopes targeted by cytotoxic T lymphocytes (CTLs). In several cases, mutations at epitopes recognized by the patient's own major histocompatibility complex (MHC) appeared after infection, but reversion of transmitted mutations was rarely seen. These data indicate that acute HIV-1 (subtype B) infection usually results from transmission of a single viral variant carrying mutations in CTL epitopes and that selection of revertants can be very slow. These results have important implications for the use of CTL-based vaccine strategies and will aid in understanding the basic mechanisms of HIV evolution and emergence of immune resistance.