A genome-to-genome analysis of associations between human genetic variation, HIV-1 sequence diversity, and viral control.

Highly significant associations were observed between SNPs in the major histocompatibility complex (MHC) region and multiple amino acids throughout the HIV-1 proteome (except in Vpu, Rev and the RNaseH subunit of RT) ( Figure 2C ), with Gag and Nef having a significantly higher density of associated variable sites than the rest of the proteome (Gag: 6.8% vs 2.6% p=0.001; Nef: 11% vs 2.6% p = 1.2 × 10 −5 , binomial tests).

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