@Article {export:80545, abstract = {  Human immunodeficiency
virus type 1 (HIV-1) mutations that confer escape from cytotoxic
T-lymphocyte (CTL) recognition can sometimes result in lower
viral fitness. These mutations can then revert upon transmission
to a new host in the absence of CTL-mediated immune selection
pressure restricted by the HLA alleles of the prior host. To
identify these potentially critical recognition points on the
virus, we assessed HLA-driven viral evolution using three
phylogenetic correction methods across full HIV-1 subtype C
proteomes from a cohort of 261 South Africans and identified
amino acids conferring either susceptibility or resistance to
CTLs. A total of 558 CTL-susceptible and -resistant HLA-amino
acid associations were identified and organized into 310
immunological sets (groups of individual associations related to
a single HLA/epitope combination). Mutations away from seven
susceptible residues, including four in Gag, were associated
with lower plasma viral-RNA loads (q Gag