Contending with the Challenges of HIV Genetic Diversity: The Role of Epitope Variant Recognition in Immune Control of HIV

Abstract

Despite over 30 years of intensive research, the development of an effective HIV vaccine has remained elusive. One of the most significant challenges in designing an HIV vaccine is contending with the extensive sequence variability found in circulating virus strains. An HIV vaccine will likely require the induction of both HIV-specific antibodies and cytotoxic T lymphocyte (CTL) responses. The efficacy of future HIV vaccines will likely depend on the ability of the induced immune effectors to cope with this widespread sequence diversity. In this thesis, I focused on investigating the capacity of HIV-specific T cells to handle genetic variation during natural HIV infection. In my first aim, I sought to determine the role of epitope variant recognition in immune control of HIV. To this end, I comprehensively assessed epitope variant recognition in HIV-infected subjects with and without spontaneous control of viral replication by testing for T-cell responses to all Gag variants present in at least 5% of sequences found in the Los Alamos National Laboratory HIV Sequence Database using IFNγ/IL-2 FluoroSpot. Contrary to my expectations, I found that the observed levels of variant recognition were directly associated with viral load, and thus individuals with progressive infection demonstrated a marginally higher ability to recognize epitope variants. However, increased sequence coverage, defined as the overall proportion of HIV database sequences targeted through the Gag-specific repertoire, was found to be inversely associated with viral load. These results highlight that it is the ability to target the most frequently occurring variants, rather than simply a large number of variants, that is associated with control of viral replication. In my second aim, I studied dynamic CTL escape processes following primary HIV infection, with an emphasis on exploring the immune pressure mediated by early cross-reactive CTL responses. In this work, I screened for T-cell responses by IFNγ/IL-2 FluoroSpot using autologous peptide sets reflecting any variant present in at least 5% of Gag sequence reads from six linked HIV transmission pairs. Escape processes were found to be highly variable, with limited overlap in the patterns of escape between individuals. By testing for responses to variants that emerged in the viral population over time, I found that 70% of responses to evolving epitopes demonstrated some degree of epitope variant recognition. Interestingly, the variants that persisted in the viral population were recognized with a significantly lower functional avidity than responses to founder sequence, suggesting functional avidity as a surrogate for effective variant recognition. Several vaccine strategies designed to induce T-cell responses of enhanced variant recognition capacity are currently moving into phase I clinical trials. Taken together, these results provide evidence for sequence coverage and functional avidity to serve as critical measures to determine the protective potential of variant-inclusive vaccines.