Immune Evasion and Viral Replication: Examining the Pressures that Influence the Evolution of CD8+ T-cell Epitope Sequences During HIV Infection

The evolution of immune escape during HIV infection is well documented, yet some CD8+ T-cell epitopes remain conserved even in the presence of strong cognate responses. This report investigates the frequency of sequence variability within the HLA-A2 restricted immunodominant epitope SLYNTVATL (SL9). Sequencing results, from 15 HIV+ HLA-A2+ individuals, support a very high degree of conservation of this epitope sequence with only focused, conservative changes evident in proviral quasispecies. These observations suggest that changes to the SL9 sequence may have deleterious effects on viral replication and are therefore limited in vivo. To investigate the sequence constraints imposed on the SL9 epitope by HIV replicative fitness, HIV plasmid clones incorporating synonymous and non-synonymous mutations throughout the SL9 epitope region were constructed. Growth of the resultant congenic viruses in mono-infection assays indicated a wide diversity of SL9 variant viruses that grew efficiently. Furthermore, dual-infection viral competition assays demonstrated that SL9 variants known to arise in vivo were equally fit to consensus SL9 virus and several novel epitope variants were also able to compete effectively. Collectively, the data reported in this thesis reveal that the viral pressures acting to conserve the SL9 epitope sequence are less than previously assumed and highlight the lack of understanding of protective CD8+ T-cell action during HIV infection.Ph