Maintenance of viral suppression in HIV-1-infected HLA-B*57+ elite suppressors despite CTL escape mutations

Abstract

Rare human immunodeficiency virus 1-infected individuals, termed elite suppressors (ES), maintain plasma virus levels of <50 copies/ml and normal CD4 counts without therapy. The major histocompatibility complex class I allele group human histocompatibility leukocyte antigen (HLA)-B*57 is overrepresented in this population. Mutations in HLA-B*57-restricted epitopes have been observed in ES, but their significance has remained unclear. Here we investigate the extent and impact of cytotoxic T lymphocyte (CTL) escape mutations in HLA-B*57+ ES. We provide the first direct evidence that most ES experience chronic low level viremia. Sequencing revealed a striking discordance between the genotypes of plasma virus and archived provirus in resting CD4+ T cells. Mutations in HLA-B*57-restricted Gag epitopes were present in all viruses from plasma but were rare in proviruses, suggesting powerful selective pressure acting at these epitopes. Surprisingly, strong CD8+ T cell interferon-gamma responses were detected against some mutant epitopes found in plasma virus, suggesting the development of de novo responses to viral variants. In some individuals, relative CD8+ T cell interleukin-2 responses showed better correlation with the selection observed in vivo. Thus, analysis of low level viremia reveals an unexpectedly high level of CTL escape mutations reflecting selective pressure acting at HLA-B*57-restricted epitopes in ES. Continued viral suppression probably reflects CTL responses against unmutated epitopes and residual or de novo responses against epitopes with escape mutations.

Figure 1.

Sequences of HLA-B*57–restricted Gag epitopes and other CTL epitopes in gag genes amplified from proviral DNA and plasma of ES. Areas shaded in blue are optimal HLA-B*57–restricted epitopes. Areas shaded in yellow are non–HLA-B*57–restricted epitopes that stimulate CD8⁺ T cell IFN-γ responses in that individual. Intervening gag sequence between these epitopes is not shown. The first sequence of each group is the gag clade B consensus sequence. Homology to this sequence is indicated by a dot. Stop codons are indicated by an asterisk (*) in place of an amino acid. Asterisks in the “Source” column indicate sequences from resting CD4⁺ T cells with characteristic APOBEC3G-mediated G→A hypermutation. Sequences are listed in the following order: hypermutated proviral sequences, nonhypermutated proviral sequences, and sequence from plasma virus.

Figure 1.

Sequences of HLA-B*57–restricted Gag epitopes and other CTL epitopes in gag genes amplified from proviral DNA and plasma of ES. Areas shaded in blue are optimal HLA-B*57–restricted epitopes. Areas shaded in yellow are non–HLA-B*57–restricted epitopes that stimulate CD8⁺ T cell IFN-γ responses in that individual. Intervening gag sequence between these epitopes is not shown. The first sequence of each group is the gag clade B consensus sequence. Homology to this sequence is indicated by a dot. Stop codons are indicated by an asterisk (*) in place of an amino acid. Asterisks in the “Source” column indicate sequences from resting CD4⁺ T cells with characteristic APOBEC3G-mediated G→A hypermutation. Sequences are listed in the following order: hypermutated proviral sequences, nonhypermutated proviral sequences, and sequence from plasma virus.

Figure 2.

CD8⁺ T cell IFN-γ responses, expressed as SFCs per million PBMCs, to wild-type forms of well-defined HLA-B*57–restricted epitopes in all HIV-1 genes and responses to non-B57–restricted overlapping peptides spanning the entire gag gene. The first four peptides shown in Gag (IW9, KF11, TW10, and QW9) are HLA-B^*57 restricted. Epitopes that are mutated in all plasma virus gag genes from that individual are indicated by an asterisk (^*).

Figure 3.

IFN-γ responses to autologous mutant epitopes. IFN-γ responses by CD8⁺ T cells from each subject against wild-type targeted epitopes and mutant epitopes found in plasma virus or minor proviral populations in that individual. •, responses against wild-type epitopes; ◯, responses to plasma virus mutant epitopes. (A–C) Responses by ES8 to wild-type and mutant IW9, TW10, and EH15. (D and E) Responses by ES2 to wild-type and mutant IW9 and TW10. (F and G) Responses by ES3 to wild-type and mutant IW9 and TW10. (H and I) Responses by ES9 to wild-type and mutant KF11 and KK10. (J and K) Responses by ES7 to wild-type and mutant IW9 and TW10. (L and M) Responses by ES6 to wild-type and mutant IW9 and TW10.

Figure 4.

IFN-γ responses to nonautologous mutant epitopes. IFN-γ responses against wild-type and mutant epitopes by CD8⁺ T cells from subjects whose virus does not have the mutation being tested. The subject providing PBMCs is indicated above each graph. •, responses against wild-type epitopes; ◯, responses to mutant epitopes. (A) Responses to wild-type TW10 and Q244T/I247V/G248A plasma virus mutant of TW10. (B) Responses to TW10 and G248E variant. (C) Responses to TW10 and E245A variant. (D) Responses to KF11 and A163S variant. (E) Responses to IW9 and I147M variant. (F) Responses to IW9 and I147L variant. Similar responses to these epitopes by additional subjects are shown in Fig. S1.

Figure 5.

IL-2 responses to autologous mutant epitopes. IL-2 responses by CD8⁺ T cells from each subject against wild-type targeted epitopes and mutant epitopes found in plasma virus or minor proviral populations in that individual. •, responses against wild type epitopes; ◯, responses to plasma virus mutant epitopes.