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.

FIG. 1.

Validation of obtained chimeric NL4-3 sequences by phylogenetic analysis. The tree was drawn by the maximum-likelihood method (Proml, PHYLIP) using entire Gag protein sequences. Blue taxa indicate sequences from chimeric viral stocks. Red taxa indicate the original plasma viral sequence. Note that all viral stocks and plasma viral sequences from the same subjects shared the same branches.

FIG. 2.

Comparison of VRCs of gag-protease chimeric viruses between EC and CP. VRCs of chimeric NL4-3 were compared among 54 EC and 41 CP. (A) Kinetics of viral replication; red and black lines indicate EC and CP, respectively. Representative data from duplicate experiments are shown. (B) Comparison of the slope of the natural log between day 2 and day 6. Data shown here are the averages of duplicate experiments. Dashed line indicates VRC of wild-type NL4-3.

FIG. 3.

Comparison of VRC between EC and CP by HLA alleles. VRC of chimeric NL4-3 was compared between EC and CP in the context of the designated class I HLA alleles. (A) B*57 versus non-B*57; (B) protective (B*27, B*51, and B*57) alleles versus others; (C) A*02 versus others; (D) B*07 versus others; (E) A*02 versus others after removal of B*57; (F) A*02 or B*07 versus others after removal of B*57.