Evidence of Differential HLA Class I-Mediated Viral Evolution in Functional and Accessory/Regulatory Genes of HIV-1

Abstract

Despite the formidable mutational capacity and sequence diversity of HIV-1, evidence suggests that viral evolution in response to specific selective pressures follows generally predictable mutational pathways. Population-based analyses of clinically derived HIV sequences may be used to identify immune escape mutations in viral genes; however, prior attempts to identify such mutations have been complicated by the inability to discriminate active immune selection from virus founder effects. Furthermore, the association between mutations arising under in vivo immune selection and disease progression for highly variable pathogens such as HIV-1 remains incompletely understood. We applied a viral lineage-corrected analytical method to investigate HLA class I-associated sequence imprinting in HIV protease, reverse transcriptase (RT), Vpr, and Nef in a large cohort of chronically infected, antiretrovirally naïve individuals. A total of 478 unique HLA-associated polymorphisms were observed and organized into a series of “escape maps,” which identify known and putative cytotoxic T lymphocyte (CTL) epitopes under selection pressure in vivo. Our data indicate that pathways to immune escape are predictable based on host HLA class I profile, and that epitope anchor residues are not the preferred sites of CTL escape. Results reveal differential contributions of immune imprinting to viral gene diversity, with Nef exhibiting far greater evidence for HLA class I-mediated selection compared to other genes. Moreover, these data reveal a significant, dose-dependent inverse correlation between HLA-associated polymorphisms and HIV disease stage as estimated by CD4+ T cell count. Identification of specific sites and patterns of HLA-associated polymorphisms across HIV protease, RT, Vpr, and Nef illuminates regions of the genes encoding these products under active immune selection pressure in vivo. The high density of HLA-associated polymorphisms in Nef compared to other genes investigated indicates differential HLA class I-driven evolution in different viral genes. The relationship between HLA class I-associated polymorphisms and lower CD4+ cell count suggests that immune escape correlates with disease status, supporting an essential role of maintenance of effective CTL responses in immune control of HIV-1. The design of preventative and therapeutic CTL-based vaccine approaches could incorporate information on predictable escape pathways.

Host-Specific Adaptation of HIV-1 Subtype B in the Japanese Population

“…Consistent with previous studies of HLA-APs in HIV clade B (2,16,18), HLA-APs were more frequently detected in Nef than in Gag and Pol. Also consistent with previous observations in Caucasian, African, Chinese, and Mexican populations (1,6,11,15,18), the number of HLA-B-associated polymorphisms in our cohort was higher than that of HLA-A-or HLA-C-associated polymorphisms, further supporting a dominant role of HLA-B in HIV evolution (32). An interesting feature of the Japanese population is that approximately 70% of individuals carry HLA-A*24:02 (23).…”

“…HLA-APs were more frequently detected in Nef (occurring at 45 of 206 codons [21.8%]) compared to Gag (51 of 500 codons [10.2%]) or Pol (51 of 947 codons [5.1%]). Although HLA class I allele frequencies in Japan are somewhat distinct globally, the distribution of HLA-APs across HIV-1 proteins was consistent with that reported in previous studies of other populations infected with clade B or C (1,2,6,7,16). Broken down by HLA locus, the numbers of HLA-A-, HLA-B-, and HLA-C-associated polymorphisms were 78, 140, and 66, respectively, numbers that were also consistent with previous reports from Caucasian and African cohorts that HLA-B alleles restrict more associations than HLA-A or HLA-C alleles (1,6,18).…”

“…HLA-APs can be identified in large cross-sectional linked data sets of host (HLA) and HIV genotypes using statistical-association approaches that identify viral polymorphisms significantly over-or underrepresented in individuals harboring a specific HLA class I allele (1,2,4,(16)(17)(18)21). HLA-APs that are overrepresented in individuals harboring the relevant HLA are commonly referred to as "adapted" forms, while those underrepresented in individuals harboring the relevant HLA are referred to as "nonadapted" forms (2,18).…”

“…H IV cytotoxic T lymphocyte (CTL) escape occurs in a manner that is highly reproducible in the context of the HLA class I alleles expressed by the host (1)(2)(3)(4)(5)(6)(7)(8). By extension, HIV sequences circulating in a given host population exhibit polymorphisms that reflect the HLA allele distribution of that population (9).…”

Phylogenetic Analysis of Population-Based and Deep Sequencing Data to Identify Coevolving Sites in the nef Gene of HIV-1

“…Full-length sequences of HIV-1 nef were amplified using nested RT-PCR and sequenced following the procedure described previously by Alexander et al (2001). Further details and GenBank accession numbers for the bulk sequences can be found in Brumme et al (2007).…”