@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 > Rev > Pol > Nef > Vif > Tat > Env > Vpu (Fisher's exact test; P [&le;] 0.0009 for each comparison), suggesting the same ranking of fitness costs by genes associated with CTL escape. Significantly more HLA-B (chi2; P=3.59 x 10-5) and HLA-C (chi2; P=4.71 x 10-6) alleles were associated with amino acid changes than HLA-A, highlighting their importance in driving viral evolution. In conclusion, specific HIV-1 residues (enriched in Vpr, Gag, and Rev) and HLA alleles (particularly B and C) confer susceptibility to the CTL response and are likely to be important in the development of vaccines targeted to decrease the viral load.

}, author = {Christine M. Rousseau and Marcus G. Daniels and Jonathan M. Carlson and Carl Kadie and Hayley Crawford and Andrew Prendergast and Philippa Matthews and Rebecca Payne and Morgane Rolland and Dana N. Raugi and Brandon S. Maust and Gerald H. Learn and David C. Nickle and Hoosen Coovadia and Thumbi Ndung'u and Nicole Frahm and Christian Brander and Bruce D. Walker and Philip J. R. Goulder and Tanmoy Bhattacharya and David E. Heckerman and Bette T. Korber and James I. Mullins}, journal = {Journal of Virology}, number = {13}, pages = {6434-6446}, title = {HLA Class I-Driven Evolution of Human Immunodeficiency Virus Type 1 Subtype C Proteome: immune Escape and Viral Load}, url = {http://research.microsoft.com/apps/pubs/default.aspx?id=80545}, volume = {82}, year = {2008}, }