Background:
During an analytic treatment interruption (ATI), the elimination of HIV-infected cells by HIV-specific cytotoxic CD8 T cells (CTLs) is required to control viral infection. However, unless treatment is initiated during acute infection, the HIV reservoir becomes dominated by CTL escape variants resistant to immune response. To address this issue, we applied a novel IMmunoinformatics Analysis Pipeline (IMAP) to identify CTL epitopes within structurally important HIV protein regions that avoid CTL immune escape mutations.
Methods:
Employing the IMAP, we generated 8-14 mer overlapping peptides containing amino acid residues that are essential for HIV Gag protein structure and function. We excluded the peptides containing CTL escape mutations and those found within < 85% of all HIV-1 subtypes/recombinants. Using the Immune Epitope Database and NetMHCpan analysis tools, we selected the peptides that are predicted to be immunogenic and are binders to multiple HLA-I alleles. These peptides were compared to the Gag protein region extracted from HIV RNA sequences of five participants who underwent multiple ATIs.
Results:
We identified a total of 32 overlapping peptides within the Gag protein from positions 150-166. Interestingly, when we compared this protein region to the Los Alamos HIV database, we observed 55% of the HIV sequences contained arginine (R) and 41% contained lysine (K) at position 154. Therefore, the R/K variant peptides combined (n=24) were identified within 96% of viral sequences worldwide. Of note, none of these peptides contained the R/K variations at positions critical for HLA-I anchoring. Eight additional overlapping HIV peptides identified within positions 155-166 of the Gag protein region were found within 95% of HIV sequences globally. These 32 HIV peptides were predicted to bind to multiple HLA-I alleles, resulting in 88% worldwide population coverage. When including the R/K variant forms of the HIV peptides, 100% of plasma-derived HIV RNA sequences from 5 participants, who experienced 3 separate treatment interruptions, contained our selected Gag peptides.
Conclusions:
Applying the IMAP, we defined novel HIV peptides within a structurally important region of the Gag protein. Importantly, these peptides were genetically conserved and avoid known CTL escape mutations. The peptides were identified within ATI-derived plasma HIV RNA sequences, indicating these peptides as a pool are highly promising for eliciting a CD8 T cell immune response during treatment interruption.