Brockman MA , Brumme ZL , Brumme CJ , Miura T , Sela J , Rosato PC , Kadie CM , Carlson JM , Markle TJ , Streeck H , Kelleher AD , Markowitz M , Jessen H , Rosenberg E , Altfeld M , Harrigan PR , Heckerman D , Walker BD , Allen TM
J Virol.2010 Sep 1 ; ():.
PMID: 20810731[PubMed - as supplied by publisher]
Mutations that allow escape from CD8 T cell responses are common in HIV-1 and may attenuate pathogenesis by reducing viral fitness. While this has been demonstrated for individual cases, a systematic investigation of the consequence of HLA class I-mediated selection on HIV-1 in vitro replication capacity (RC) has not been undertaken. We examined this question by generating recombinant viruses expressing plasma HIV-1 RNA-derived Gag-Protease sequences from 66 acute/early and 803 chronic untreated subtype B infected individuals in an NL4-3 background and measuring their RC using a GFP-reporter CD4 T cell assay. In acute/early infection, viruses derived from individuals expressing protective alleles HLA-B*57, B*58, and/or B*13 displayed significantly lower RC than viruses from individuals lacking these alleles (p<0.05). Furthermore, acute/early RC inversely correlated with the presence of HLA-B-associated Gag polymorphisms (R=-0.27, p=0.03), suggesting a cumulative effect of primary escape mutations on fitness during the first months of infection. At the chronic stage of infection, no strong correlations were observed between RC and protective HLA-B alleles or with the presence of HLA-B-associated polymorphisms restricted by protective alleles, despite increased statistical power to detect these associations. However, RC correlated positively with the presence of known compensatory mutations in chronic viruses from B*57-expressing individuals harboring Gag T242N (N=50, R=0.36, p=0.01), suggesting that rescue of fitness defects occurred through mutations at secondary sites. Additional mutations in Gag were identified that may modulate the impact of T242N on RC. A modest inverse correlation was observed between RC and CD4 cell count in chronic infection (R=-0.17, p<0.0001), suggesting that Gag-Protease RC could increase over the disease course. Notably, this association was stronger in individuals who expressed B*57, B*58, or B*13 (R=-0.27; p=0.004). Taken together, these data indicate that certain protective HLA alleles contribute to early defects in HIV-1 fitness through selection of detrimental mutations in Gag; however, these effects wane as compensatory mutations accumulate in chronic infection. Long-term control of HIV-1 in some persons who express protective alleles suggests that early fitness hits may provide lasting benefit.