Background:  To assess cytotoxic T lymphocyte (CTL) recognition of autologous HIV-1 variants we analyzed the nef-specific CTL response in a group of patients after immunization with a recombinant MVA-Nef vector.

Methods:  We vaccinated 14 HIV-1⁺ patients on HAART, whose CD4 was >400 and HIV viremia was suppressed, at week 0, week 4, and week 16 with an MVA construct expressing Nef of HIV-LAI. HIV-1-specific T cells were monitored by IFN-g ELISpot. Structured treatment interruption was performed in all patients 2 weeks after the third vaccination. Autologous Nef-genes were sequenced from PHA-stimulated peripheral blood mononuclear cells (PBMC) at baseline and from autologous plasma at peak viremia. Recognition of autologous viruses was tested by IFN-g ELISpot using variant peptides and PBMC or peptide stimulated T-cell lines.

Results:  A variety of amino acid substitutions was detected within CTL epitopes that were suggestive for CTL escape mutations. Interestingly, many patients recognized their autologous viral variants as long as the mutations were located within the T-cell receptor (TCR) recognition site of the epitopes, although these mutations induced CTL escape in other patients. For example, patient #10 very efficiently recognized the A24-restricted epitope RYPLCFGWCF (with a T to C – mutation at position p5) and the B8-restricted epitope (FLRDKGGL, with a K-to-R mutation at position p3 and an E-to-D mutation at position p4), although these mutations strongly impaired recognition by RYPLTFGWCY-specific and FLKEKGGL-specific CTL from other patients. In contrast, most mutations of the anchor amino acids of recognized CTL epitopes decreased recognition by specific CTL, such as the Y-to-F substitution in the A24-restricted epitope RYPLTFGWCY.

Conclusions:  In several patients, we observed CTL recognition of autologous viral variants despite the occurrence of mutations that confer CTL escape in other patients. This suggests that the CTL response can adapt to HIV-1 sequence variation within CTL epitopes as long as the anchor positions remain conserved. Therefore, for the development of polytope vaccines it is important to focus on CTL epitopes with conserved anchor amino acids.