Uncommon pathways of immune escape attenuate HIV-1 integrase replication capacity

An attenuation of the HIV-1 replication capacity (RC) has been observed for immune-mediated escape mutations in Gag restricted by protective HLA alleles. However, the extent to which escape mutations affect other viral proteins during natural infection is not well understood. We generated recombinant viruses encoding plasma HIV-1 RNA integrase sequences from antiretroviral-naive individuals with early (n = 88) and chronic (n = 304) infections and measured the in vitro RC of each. In contrast to data from previous studies of Gag, we observed little evidence that host HLA allele expression was associated with integrase RC. A modest negative correlation was observed between the number of HLA-B-associated integrase polymorphisms and RC in chronic infection (R = -0.2; P = 0.003); however, this effect was not driven by mutations restricted by protective HLA alleles. Notably, the integrase variants S119R, G163E, and I220L, which represent uncommon polymorphisms associated with HLA-C*05, -A*33, and -B*52, respectively, correlated with lower RC (all q < 0.2). We identified a novel C*05-restricted epitope (HTDNGSNF(114-121)) that likely contributes to the selection of the S119R variant, the polymorphism most significantly associated with lower RC in patient sequences. An NL4-3 mutant encoding the S119R polymorphism displayed a similar to 35%-reduced function that was rescued by a single compensatory mutation of A91E. Together, these data indicate that substantial HLA-driven attenuation of integrase is not a general phenomenon during HIV-1 adaptation to host immunity. However, uncommon polymorphisms selected by HLA alleles that are not conventionally regarded to be protective may be associated with impaired protein function. Vulnerable epitopes in integrase might therefore be considered for future vaccine strategies

Molecular and functional consequences of immune-mediated evolution in HIV-1 Nef during the North American epidemic.

Background: HLA-restricted CTL responses drive evolution of the highly immunogenic Nef protein, but the extent and functional consequences of population-level adaptation remain unclear. We have used novel historic Nef data to estimate the date and reconstruct the founder virus sequence of the North American epidemic, compare patterns of population-level HLA-associated polymorphisms over time, and assess CD4 downregulation activity of historic and modern Nef sequences. Methods: Plasma HIV-1 RNA Nef sequencing and HLA typing was performed on 241 historic specimens (1979–89). Modern published HLA/HIV datasets served as controls. Timing and sequence reconstruction of the founder Nef was performed using BEAST and HyPhy. HLA-associated polymorphisms were identified using phylogenetically-corrected methods. CD4 downregulation capacity of 52 historic vs. 52 modern Nef sequences was compared using flow cytometric methods. Results: Based on Nef sequences, the most recent common ancestor of the North American epidemic was dated to 1965. The consensus of the reconstructed founder Nef sequence differed from 2004 subtype B consensus at codons 15, 22, 51 and 178, while additional sites remained ambiguous in the reconstruction. Patterns and statistical strengths of HLA-associated polymorphisms remained generally consistent over time (e.g. A*24-associated Y135F, B*07-R71K, B*08-K94Q and B*57-H116N ranked among the strongest in historic and modern cohorts); however, a small number of polymorphisms were identified as candidates for population-level accumulation. Functional assessment of Nef revealed a modest yet statistically significant increase in CD4 downregulation capacity over time (median 0.93 vs. 1.00 in historic vs. modern sequences; p = 0.005). Conclusion: Modest population-level immune adaptation in Nef, potentially leading to modest increases in CD4 downregulation capacity, may have occurred in North America since 1979. However, the relatively high similarity between the estimated founder and modern consensus B, and the observation that CTL escape patterns have remained largely consistent over time, support Nef as a suitable target for vaccine consideration