Screening for HIV responses using optimal epitopes predicted by HLA-viral sequence polymorphism associations

HIV escapes immune recognition by mutating critical amino acid residues in known HLA-restricted epitopes. Such changes may limit the ability of ex-vivo assays to detect and map the epitopes subject to such selection in-vivo. We used HLA-associated polymorphisms in HIV generated from an analysis of a combined cohort of 800 anti-retroviral naïve, HLA-diverse, predominantly subtype B-infected individuals from the US and Western Australia to predict and map HIV-specific T cell responses. A novel epitope prediction program Epipred was used to predict optimal length epitopes around sites of HLA-allele specific polymorphism and these were tested in IFN-γ ELISpot assays, taking into account the autologous HLA genotype and the autologous viral sequence of 200 US cohort individuals. The Elispot assay was optimised and automated for high-throughput testing of multiple HLA-customised plates. On average, 11 epitopes were tested for each patient and of these 16% elicited an IFNγ response. In an analysis of the first 29 individuals tested in this system, nine putative novel epitopes were detected. In many instances, the HLA-driven change led to loss of reactivity as predicted for classical CD8 T cell escape, however more complex patterns of reactivity were seen, particularly in Nef epitopes. The creation of an escape variant was shown to still stimulate IFNγ responses, including similar or higher magnitude responses compared with the non-adapted epitopes. The screening strategy was based on a genetics directed approach, in which specific sites and epitopes were tested based on their in-vivo polymorphism. The results have enabled us to identify possible novel epitopes that warrant further investigation using confirmatory assays. At a population level, such screening takes into account the most prevalent HLA genotypes and HLA-restricted responses in that population efficiently. These results provide further insights into CD8 T cell responses against HIV and have implications for HIV vaccine design