Background: Identity of epitope-specific CD8⁺ T-cell responses to subtype C Nef is important for clade-specific vaccine development. We report on Nef-specific CD8⁺ T-cell responses of subtype C HIV-1 infected southern Africans restricted by HLA alleles common to this region.

Method: A combination of the IFNγ ELISpot assay and intracellular cytokine staining was used to identify regions within Nef which elicit CD8⁺ T-cell responses from 60 subtype C HIV-1 infected individuals from southern Africa.

Results: Forty (40) of 60 (67%) individuals screened gave a response to Nef, with the majority of these targeting the highly conserved central region. Five (5) immunodominant peptide regions were identified; VP-15 (30%), YG-15 (28%), PA-15 (20%), IY-15 (15%), WY-15 (13%) spanning the region from amino acid position 70 to 150 and containing previously described subtype B epitopes. The frequency of HLA alleles shown to restrict these epitopes in subtype B infections is very low in Africans, suggesting that epitopes within these peptides were restricted by novel HLA alleles. HLA associations based on ELISPOT data was used to predict restricting alleles; 6/7 (86%) individuals recognizing to the YG-15 mer expressed HLA A30 and 6/8 (75%) recognizing to VP-15 expressed HLA A23, suggesting that these are the restricting alleles. The predicted alleles were confirmed using ICS; for example, in 2 individuals (525-17-1 and 616-44-5) who responded to the YG-15 peptide, we demonstrated that the epitope lying within this peptide was restricted by HLA-A30.

Conclusion: The central region of Nef is highly targeted by CD8⁺ T-cells. This region is highly conserved between clades B and C, and therefore, one can predict that previously described subtype B-defined epitopes are targeted in subtype C infected individuals. However, the disparity in HLA alleles between Caucasians and southern Africans will dictate which epitopes within this conserved region will be restricted by southern Africans infected with a clade C virus. Even though there are different HLA alleles restricting epitopes within this region, these findings show that this conserved epitope-rich region of Nef would be an attractive component to be included in candidate cross-clade vaccines.