HLA-Associated Alterations in Replication Capacity of Chimeric NL4-3 Viruses Carrying gag-protease from Elite Controllers of Human Immunodeficiency Virus Type 1

Abstract

Human immunodeficiency virus type 1 (HIV-1)-infected persons who maintain plasma viral loads of <50 copies RNA/ml without treatment have been termed elite controllers (EC). Factors contributing to durable control of HIV in EC are unknown, but an HLA-dependent mechanism is suggested by overrepresentation of "protective" class I alleles, such as B*27, B*51, and B*57. Here we investigated the relative replication capacity of viruses (VRC) obtained from EC (n ‫؍‬ 54) compared to those from chronic progressors (CP; n ‫؍‬ 41) by constructing chimeric viruses using patient-derived gag-protease sequences amplified from plasma HIV RNA and inserted into an NL4-3 backbone. The chimeric viruses generated from EC displayed lower VRC than did viruses from CP (P < 0.0001). HLA-B*57 was associated with lower VRC (P ‫؍‬ 0.0002) than were other alleles in both EC and CP groups. Chimeric viruses from B*57 ؉ EC (n ‫؍‬ 18) demonstrated lower VRC than did viruses from B*57 ؉ CP (n ‫؍‬ 8, P ‫؍‬ 0.0245). Differences in VRC between EC and CP were also observed for viruses obtained from individuals expressing no described "protective" alleles (P ‫؍‬ 0.0065). Intriguingly, two common HLA alleles, A*02 and B*07, were associated with higher VRC (P ‫؍‬ 0.0140 and 0.0097, respectively), and there was no difference in VRC between EC and CP sharing these common HLA alleles. These findings indicate that cytotoxic T-lymphocyte (CTL) selection pressure on gag-protease alters VRC, and HIV-specific CTLs inducing escape mutations with fitness costs in this region may be important for strict viremia control in EC of HIV.

HIV-specific CD8+ T cells and HIV eradication

“…Genetic studies indicate that HLA class I alleles are associated with differences in set-point viremia (15,16), modulated by the nature of viral peptide binding to the class I groove (16). Studies of viral fitness indicate that CD8 + T cell-induced mutations can diminish viral fitness, particularly those in epitopes restricted by protective HLA alleles such as B*27 and B*57, suggesting a persisting antiviral effect, even in cases of immune escape (17)(18)(19). Together, these studies indicate that CD8 + T cells are capable of potent antiviral function and provide a strong rationale for enlisting these responses in eradication strategies.…”

Impaired Nef Function Is Associated with Early Control of HIV-1 Viremia

“…In vitro viral replication capacity independently associates with early clinical markers of pathogenesis (17). Moreover, Gag, Pol, and Nef proteins from chronically infected EC have consistently displayed relative functional attenuation (18)(19)(20)(21), suggesting that impaired viral function is a hallmark of this phenotype (22). In many cases, host expression of protective HLA alleles or the presence of specific HLA-associated escape mutations or both are associated with even lower viral protein function in these individuals, suggesting that adaptation to host HLA-restricted CTL can further attenuate HIV-1.…”

HIV-1 Conserved-Element Vaccines: Relationship between Sequence Conservation and Replicative Capacity

“…Understanding of how well these cases translate at the population level has been sought with comparisons of the relative fitness, measured by replicative capacity or competitive growth assays in cell culture (10)(11)(12)(13)(14) of HIV-1 strains with gag-pro or pol inserts from both elite controllers and viremic subjects (15)(16)(17)(18)(19)(20). While the growth in any particular cell culture does not fully recapitulate the environment for virus survival in vivo, the replicative capacity of viruses from controllers was lower than that of viruses with inserts from chronically infected individuals.…”

“…This effect was more flagrant with inserts from acutely compared to chronically infected subjects and has been attributed in part to the presence of HLA-associated polymorphisms in controllers and the development of compensatory mutations that restore fitness over time (15,20). These studies were performed using a subject-derived gene integrated in a common HIV-1 backbone (9,(15)(16)(17)(18)(19)(20)(21)(22)(23)(24), and thus the results are contingent on mutations that are private to each subject's viruses and the replicative capacity of these viruses reflect a combination of mutations that differs from one subject to the next. More recently, infectious molecular clones have been developed from a number of subjects (25)(26)(27)(28)(29) and these infectious molecular clones provide the best opportunity to study interactions between different mutations and subject-specific mutational pathways that are evidenced during an HIV-1 infection.…”