Using viral diversity to identify HIV-1 variants under HLA-dependent selection in a systematic viral genome-wide screen
Fig 5
HLA-HIV peptide binding prediction based on mass spectrometry eluted ligands (EL) rank (%).
A) Log odds ratio (OR) of the Average Pairwise Diversity (APD)-HLA interaction versus the Log Ratio of EL Rank of mutation/EL Rank of consensus. Upper-right section (yellow) indicates expected major histocompatibility complex (MHC) escape mutations. Labels describe HLA/HIV-variant pairs of interest (same as in Fig 1B) and the epitope position of mutation (ranging from 1 to 9). B, C) Peptides are 9-mer HIV sequences, including the mutation (dark color; Pol432R/ RT277R (B) or Rev57E (C)) or consensus (light color; Pol432K/ RT277K (B) or Rev57G (C)) at different positions (ranging from 1 to 9). The rank was categorized into strong binder (≤0.5%), weak binder (≤2.0%), and non-binder (>2.0%). Non-binding positions are omitted here. All binding prediction computations are derived from NetMHCpan-4.1.