FIG 4.

HLA-associated polymorphisms exhibiting differential selection between subtypes A1 and D. The natural logarithm of the odds ratio (lnOR) of selection of HLA-associated polymorphisms in Gag, Nef, protease, reverse transcriptase, and integrase that were differentially selected between subtypes A1 and D are shown. The lnOR of a specific association is shown only if it was independently statistically significant in a given HIV subtype; otherwise, it was set to 0. In most cases, differential selection of an HLA-associated polymorphism occurred because the polymorphism was selected in one subtype but not the other (e.g., B*57:03-Gag T242N was significantly selected in subtype D with an lnOR of 5.6 but not in subtype A1). A small filled circle denotes cases where the same HIV polymorphism was selected at significantly different strengths in the two subtypes. For example, HLA-C*07:01 selects for Nef K105R in subtype A1 (lnOR= 2.3) but more strongly in subtype D (lnOR= 6). Polymorphisms differentially selected at a false discovery rate threshold of a q value of <0.1 and a P value of <0.05 are shown. Infinite positive or negative lnORs were set to 6 or −6, respectively, for visualization purposes.