Objectives: Both antiretroviral drugs and cytotoxic T-lymphocytes (CTL) exert selective pressure on HIV. Antiretroviral drug-resistance mutations create a major obstacle to effective long-term therapy of HIV infection. Therefore, therapeutic HIV vaccines should engage both immune and antiretroviral selection pressures, while CTL-inducing prophylactic vaccines should address transmission of drug-resistant variants. This study aims to identify drug-resistance mutations within CTL epitopes in HIV-1 pol that sustain recognition by CD8⁺ T-cells.

Methods: A recombinant vaccinia virus expressing HIV-1 pol was used in cytotoxicity assays to screen subjects for pol-specific CTL. Eighteen (18) 9–11-mer peptides representing 5 wild-type pol CTL epitopes and corresponding drug resistant variants were used in both cytotoxicity and IFN-γ ELISpot assays to test for recognition of epitopes containing drug resistance mutations.

Results: In at least 1/3 of cases, pol-specific CTL were directed against 1 or more of the selected peptides. Responses against 3 wild-type peptides restricted by HLA-A2, -A3, and -B44 and 3 corresponding variant peptides containing drug-resistance mutations were detected by cytolytic and IFN-γ ELISpot assays. Responses against the variant peptides were observed at frequencies up to 1/1000 PBMCs. In some cases, there was cross-reactive recognition of wild-type and variant peptides, whereas in other cases recognition was selective for one or the other. In vitro re-stimulation of donor PBMCs with either the wild-type peptide ALVEICTEM or variant peptide ALVEICTEL, containing the zidovudine-resistance mutation M41L, expanded CTL cross-reactive against both peptides. Specificity of the expanded CTL population for this variant peptide was confirmed by tetramer staining.

Conclusion: Antiretroviral drugs targeting HIV-1 pol select for drug-resistance mutations within protease and reverse transcriptase. Identification of strong CTL responses against 3 variant pol peptides incorporating drug-resistance mutations demonstrates that some mutations sustain or even enhance recognition by CD8⁺ T-cells. Since the variant peptide epitopes identified are presented by common HLA types, it may be possible to design broadly applicable epitope-based HIV vaccines to prevent emergence or transmission of drug-resistant variants.