Pol-Driven Replicative Capacity Impacts Disease Progression in HIV-1 Subtype C Infection

Abstract

CD8 T cell-mediated escape mutations in Gag can reduce HIV-1 replication capacity (RC) and alter disease progression, but less is known about immune-mediated attenuation in other HIV-1 proteins. We generated 487 recombinant viruses encoding RT-integrase from individuals with chronic ( = 406) and recent ( = 81) HIV-1 subtype C infection and measured their RC using a green fluorescent protein (GFP) reporter T cell assay. In recently infected individuals, reverse transcriptase (RT)-integrase-driven RC correlated significantly with viral load set point ( 0.25; = 0.03) and CD4 T cell decline ( = 0.013). Moreover, significant associations between RT integrase-driven RC and viral load ( = 0.28; < 0.0001) and CD4 T cell count ( = -0.29; < 0.0001) remained in chronic infection. In early HIV infection, host expression of the protective HLA-B*81 allele was associated with lower RC ( = 0.05), as was expression of HLA-B*07 ( = 0.02), suggesting early immune-driven attenuation of RT-integrase by these alleles. In chronic infection, HLA-A*30:09 (in linkage disequilibrium with HLA-B*81) was significantly associated with lower RC ( = 0.05), and all 6 HLA-B alleles with the lowest RC measurements represented protective alleles, consistent with long-term effects of host immune pressures on lowering RT-integrase RC. The polymorphisms V241I, I257V, P272K, and E297K in reverse transcriptase and I201V in integrase, all relatively uncommon polymorphisms occurring in or adjacent to optimally described HLA-restricted cytotoxic T-lymphocyte epitopes, were associated with reduced RC. Together, our data suggest that RT-integrase-driven RC is clinically relevant and provide evidence that immune-driven selection of mutations in RT-integrase can compromise RC. Identification of viral mutations that compromise HIV's ability to replicate may aid rational vaccine design. However, while certain escape mutations in Gag have been shown to reduce HIV replication and influence clinical progression, less is known about the consequences of mutations that naturally arise in other HIV proteins. Pol is a highly conserved protein, but the impact of Pol function on HIV disease progression is not well defined. Here, we generated recombinant viruses using the RT-integrase region of Pol derived from HIV-1C-infected individuals with recent and chronic infection and measured their ability to replicate We demonstrate that RT-integrase-driven replication ability significantly impacts HIV disease progression. We further show evidence of immune-mediated attenuation in RT-integrase and identify specific polymorphisms in RT-integrase that significantly decrease HIV-1 replication ability, suggesting which Pol epitopes could be explored in vaccine development.

Association between the cytokine storm, immune cell dynamics, and viral replicative capacity in hyperacute HIV infection

“…In agreement with a previous study that reported a relationship between viral replicative fitness and the magnitude of the inflammatory response in untreated AHI, we observed positive correlations between Gag-proteasedriven replicative capacity and the cytokines IP-10 and IFN-alpha [31]. Other studies have reported faster CD4 + T cell decline in patients who are infected with fasterreplicating viruses, an effect that could be driven by the strong inflammatory response induced by the fitter viruses [31,32]. Thus, modulating inflammatory cytokines could reduce CD4 + T cell depletion in AHI with possible benefits as the patients progress into the chronic phase.…”

“…As expected, the transmitted/founder viruses among untreated participants differed among individuals with regard to Gag-protease-driven replicative capacities ( Fig. 4a) and nucleotide sequences (Supplementary figure 2A-B) [29,32]. Notably, most of the transmitted/founder viruses had attenuating polymorphisms that have been previously shown to reduce Gag-protease-driven replicative capacity [32].…”

“…4a) and nucleotide sequences (Supplementary figure 2A-B) [29,32]. Notably, most of the transmitted/founder viruses had attenuating polymorphisms that have been previously shown to reduce Gag-protease-driven replicative capacity [32]. Interestingly, we observed a trend of an inverse correlation between the total numbers of attenuating polymorphisms and Gag-protease-driven replicative capacities (rho = − 0.56, P = 0.067) (Supplementary figures 2C).…”

Infection with multiple HIV-1 founder variants is associated with lower viral replicative capacity, faster CD4+ T cell decline and increased immune activation during acute infection

“…These highly unequal proportions of TF viruses at acute infection suggest different replication advantages among TF viruses in the same HIV-1-infected individuals. We therefore measured the replicative capacity conferred by TF gag sequences of both major and minor variants, which has previously been shown to correlate closely to that of the entire full length infectious molecular clone, and to be predictive of disease progression [ 26 , 31 , 32 ].…”

HIV-1 Gag-Pol Sequences from Ugandan Early Infections Reveal Sequence Variants Associated with Elevated Replication Capacity

“…We asked if there were differences in VRC among Ugandan HIV-1 early viruses of subtypes A and D and their recombinants and set out to identify virus sequence features that might account for differences in VRC. The HIV-1 gag and pol genes are among the most conserved of the HIV-1 genome and in subtype C viruses appear to drive replication capacity and clinical outcomes [ 14 , 20 ]. Moreover, Gag-Pol chimeric viruses were shown to display similar VRC as the full-length HIV-1 genomes from which they were derived, supporting the idea that the Gag-Pol region was a major determinant of VRC.…”