Figure S1 - CD8+ T Cell Cross-Reactivity Profiles and HIV-1 Immune Escape towards an HLA-B35-Restricted Immunodominant Nef Epitope

CPL scanning of VY8-specific CD8+ T cells. The cross-reactivity profiles of T cell lines and clones specific for VY8 were tested by using 160 CPL sub-mixtures (100 µg/ml) comprising a total of 2.4×1010 different octamer peptides. In every peptide mixture, one position has a fixed amino acid residue and all other positions are degenerate, with the possibility of any one of 19 natural amino acids being incorporated in each individual position (cysteine is excluded). The amount of MIP-1β secreted in response to antigen was quantified by ELISA. Data are background-subtracted and the relative T cell response is shown as a ratio of MIP-1β production with respect to the index residue at each position. Responses >20% were considered positive and used to construct Figure 1. A representative set of duplicate assays is shown. Red bars depict residues corresponding to the VY8 index sequence. (EPS)