Matthews, Philippa C.Listgarten, JenniferCarlson, Jonathan M.Payne, RebeccaHuang, Kuan-Hsiang GaryFrater, JohnGoedhals, DominiqueSteyn, Dewaldvan Vuuren, CloetePaioni, PaoloJooste, PieterOgwu, AnthonyShapiro, RogerMncube, ZeneleNdung'u, ThumbiWalker, BruceHeckerman, DavidGoulder, Philip J. R.2013-04-082012Matthews, Philippa C., Jennifer Listgarten, Jonathan M. Carlson, Rebecca Payne, Kuan-Hsiang Gary Huang, John Frater, Dominique Goedhals, et al. 2012. Co-operative additive effects between HLA alleles in control of HIV-1. PLoS ONE 7(10): e47799.1932-6203http://nrs.harvard.edu/urn-3:HUL.InstRepos:10511100Background: HLA class I genotype is a major determinant of the outcome of HIV infection, and the impact of certain alleles on HIV disease outcome is well studied. Recent studies have demonstrated that certain HLA class I alleles that are in linkage disequilibrium, such as HLA-A*74 and HLA-B*57, appear to function co-operatively to result in greater immune control of HIV than mediated by either single allele alone. We here investigate the extent to which HLA alleles - irrespective of linkage disequilibrium - function co-operatively. Methodology/Principal Findings: We here refined a computational approach to the analysis of >2000 subjects infected with C-clade HIV first to discern the individual effect of each allele on disease control, and second to identify pairs of alleles that mediate ‘co-operative additive’ effects, either to improve disease suppression or to contribute to immunological failure. We identified six pairs of HLA class I alleles that have a co-operative additive effect in mediating HIV disease control and four hazardous pairs of alleles that, occurring together, are predictive of worse disease outcomes (q<0.05 in each case). We developed a novel ‘sharing score’ to quantify the breadth of CD8+ T cell responses made by pairs of HLA alleles across the HIV proteome, and used this to demonstrate that successful viraemic suppression correlates with breadth of unique CD8+ T cell responses (p = 0.03). Conclusions/Significance: These results identify co-operative effects between HLA Class I alleles in the control of HIV-1 in an extended Southern African cohort, and underline complementarity and breadth of the CD8+ T cell targeting as one potential mechanism for this effect.en-USBiologyImmunologyImmune CellsT CellsMedicineClinical ImmunologyImmunityAdaptive ImmunityImmune DefenseImmune ResponseMajor Histocompatibility ComplexInfectious DiseasesViral DiseasesHIVRetrovirology and HIV immunopathogenesisObstetrics and GynecologyGenitourinary InfectionsUrologyJournal Article2013-04-0810.1371/journal.pone.0047799