Spontaneous control of HIV-1 viremia in a subject with protective HLA-B plus HLA-C alleles and HLA-C associated single nucleotide polymorphisms

Abstract

Introduction: Understanding the mechanisms by which some individuals are able to naturally control HIV-1 infection is an important goal of AIDS research. We here describe the case of an HIV-1(+) woman, CASE1, who has spontaneously controlled her viremia for the last 14 of her 20 years of infection.

Methods: CASE1 has been clinically monitored since 1993. Detailed immunological, virological and histological analyses were performed on samples obtained between 2009 and 2011.

Results: As for other Elite Controllers, CASE1 is characterized by low to undetectable levels of plasma HIV-1 RNA, peripheral blood mononuclear cell (PBMC) associated HIV-1 DNA and reduced in vitro susceptibility of target cells to HIV-1 infection. Furthermore, a slow rate of virus evolution was demonstrated in spite the lack of assumption of any antiretroviral agent. CASE1 failed to transmit HIV-1 to either her sexual male partner or to her child born by vaginal delivery. Normal values and ratios of T and B cells were observed, along with normal histology of the intestinal mucosa. Attempts to isolate HIV-1 from her PBMC and gut-derived cells were unsuccessful, despite expression of normal cell surface levels of CD4, CCRC5 and CXCR4. CASE1 did not produce detectable anti-HIV neutralizing antibodies in her serum or genital mucosal fluid although she displayed potent T cell responses against HIV-1 Gag and Nef. CASE1 also possessed multiple genetic polymorphisms, including HLA alleles (B*14, B*57, C*06 and C*08.02) and HLA-C single nucleotide polymorphisms (SNPs, rs9264942 C/C and rs67384697 del/del), that have been previously individually associated with spontaneous control of plasma viremia, maintenance of high CD4(+) T cell counts and delayed disease progression.

Conclusions: CASE1 has controlled her HIV-1 viremia below the limit of detection in the absence of antiretroviral therapy for more than 14 years and has not shown any sign of immunologic deterioration or disease progression. Co-expression of multiple protective HLA alleles, HLA-C SNPs and strong T cell responses against HIV-1 proteins are the most likely explanation of this very benign case of spontaneous control of HIV-1 disease progression.

Figure 1

CASE1’s natural control of HIV-1 viremia. (A) Levels of peripheral CD4⁺ and CD8⁺ T cells, plasma viral RNA and the presence of anti-HIV-1 Ab in CASE1 plasma were monitored over 20 years of infection. Purified peripheral CD4⁺ cells were isolated from CASE1 and infected with either an R5 (B) or an X4 (C) strain, resulting in detectable virus replication. Purified CD4⁺ T cells of her sexual partner supported higher levels of virus replication. Bars indicate error of the mean from duplicate cultures.

Figure 2

Phylogenetic analysis of CASE1 HIV-1 gag and env sequences. Viral genome templates corresponding to the near full length gag gene (HXB2 nucleotides 818–2276) and the gp120 coding region of env (HXB2 nucleotides 6229–7786) were PCR amplified from blood plasma and PBMC DNA collected in June and November of 2009, and from PBMC from June 2011, as described in Additional data. PCR products derived from individual viral templates were sequenced directly and analyzed as described in Additional data. PBMC- and plasma (PL)-derived sequences are labeled by date (YYMMDD). Mutations at specific tree branches are tallied as either non-synonymous (NS) or synonymous (S). Two epitopes changed over time in gag (A). The B*57 associated AA substitution I147L in the immunodominant B*57 epitope IW9 was a reversion mutation, resulting in a susceptible, consensus form of the epitope - hence the branch extends from the CASE1 sequences earlier in infection towards the consensus. The TW10 mutation, by contrast, was an escape mutation, with the consensus of all of the Group M viruses being the susceptible form of the epitope - hence the branch extends from the CASE1 sequences earlier in infection away from the consensus. These 2 NS mutations are bolded and noted by a thick arrow between the sequences. NS mutations resulting in two potential N-linked glycosylation sites (PNLGS) were found in env (B). The scale bar below each dendrogram illustrates the branch length formed by mutations corresponding to a 1% change. Amino acid alignments are provided in Additional data.

Figure 3

T-cell responses of CASE1 T cells to Gag, Nef, and Tat peptides. (A) Recognition of Gag and Nef, but not of Tat peptide pools by CASE1 PBMC collected in June 2011. (B) Recognition of Gag pools (A-L): pools D, E, G, H, and I contain well-defined HLA-B*57 restricted Gag epitopes. (C) Identification of epitopes recognized by CASE1 contained in Gag pools D, E, H and I. The table provides the HLA-restriction, the peptide designation and its sequence. The sequence of minimal epitopes for both Gag and Nef are shown in bold. (D) PBMC isolated from CASE1 were either left unstimulated or were stimulated with Gag peptide #25 and #26 and functionality of CD8+ T assessed by means of cytofluorimetric analysis for the production of Granzyme-B (GzB), Interferon-γ (IFN-γ), CC chemokine ligand 4 (CCL4)/Macrophage Inflammatory Protein-1β (MIP-1β) and Tumor Necrosis Factor-α (TNF-α); the cell population was subdivided into the CD45RA⁺ and CD45RA^neg CD8⁺ T-cell subsets and the percentages of these subsets were calculated relative to the peptide 25 and 26 Gag-specific response. (E) Recognition of Nef overlapping peptides. The HLA-B*57 and C*06 restricted minimal epitopes contained in Nef #13 (RPMTYKAAVDLSHFLK) were: RPMTYKAAV (C*06), MTYKAAVDL (C*06), KAAVDLSHF (B*57), AAVDLSHFL (C*06); minimal epitopes in Nef #18 (LDLWIYHTQGYFPDWQNY) and Nef #19 (YHTQGYFPDWQNYT) were: HTQGYFPDW (B*57) and GYFPDWQNY (C*06). The dotted line indicates the negative cut-off of the assay.