Fine-mapping classical HLA variation associated with durable host control of HIV-1 infection in African Americans

A small proportion of human immunodeficiency virus-1 (HIV-1) infected individuals, termed HIV-1 controllers, suppress viral replication to very low levels in the absence of therapy. Genetic investigations of this phenotype have strongly implicated variation in the class I major histocompatibility complex (MHC) region as key to HIV-1 control. We collected sequence-based classical class I HLA genotypes at 4-digit resolution in HIV-1-infected African American controllers and progressors (n 1107), and tested them for association with host control using genome-wide single nucleotide polymorphism data to account for population structure. Several classical alleles at HLA-B were associated with host control, including B57:03 [odds ratio (OR) 5.1; P 3.4 10(18)] and B81:01 (OR 4.8; P 1.3 10(9)). Analysis of variable amino acid positions demonstrates that HLA-B position 97 is the most significant association with host control in African Americans (omnibus P 1.2 10(21)) and explains the signal of several HLA-B alleles, including B57:03. Within HLA-B, we also identified independent effects at position 116 (omnibus P 2.8 10(15)) in the canonical F pocket, position 63 in the B pocket (P 1.5 10(3)) and the non-pocket position 245 (P 8.8 10(10)), which is thought to influence CD8-binding kinetics. Adjusting for these HLA-B effects, there is evidence for residual association in the MHC region. These results underscore the key role of HLA-B in affecting HIV-1 replication, likely through the molecular interaction between HLA-B and viral peptides presented by infected cells, and suggest that sites outside the peptide-binding pocket also influence HIV-1 control.