Permanent control of HIV-1 pathogenesis in exceptional elite controllers: a model of spontaneous cure

Abstract

Elite controllers (EC) represent a small subset of HIV-1-infected people that spontaneously control viral replication. However, natural virological suppression and absence of immune dysfunction are not always long-term sustained. We define exceptional EC (EEC) as HIV-1 subjects who maintain the EC characteristics without disease progression for more than 25 years. We analyzed three EEC, diagnosed between 1988 and 1992, who never showed signs of clinical disease progression in absence of any antiretroviral treatment. A comprehensive clinical, virological, and immunological study was performed. The individuals simultaneously exhibited ≥3 described host protective alleles, low levels of total HIV-1 DNA (<20 copies/10⁶ CD4⁺ T-cells) without evidence of replication-competent viruses (<0.025 IUPM), consistent with high levels of defective genomes, strong cellular HIV-1-specific immune response, and a high poly-functionality index (>0.50). Inflammation levels of EEC were similar to HIV-1 negative donors. Remarkably, they showed an exceptional lack of viral evolution and 8-fold lower genetic diversity (<0.01 s/n) in env gene than other EC. We postulate that these EEC represent cases of spontaneous functional HIV-1 cure. A non-functional and non-genetically evolving viral reservoir along with an HIV-1-specific immune response seems to be key for the spontaneous functional cure.

Figure 1

Clinical characteristics and HIV-1 reservoir quantification. (A–C) Plasma RNA viral load, absolute CD4⁺ and CD4⁺ T cell percentage over time in the individuals studied. Grey symbols for viral load indicate values below the detection limit. (D–G) Viral reservoir measurements of (D) total HIV-1 DNA, (E) Infectious Units per million cells (IUPM) in a qVOA assay, (F) ultrasensitive plasma viral load and (G) cell associated RNA (caHIV-1-RNA). Open symbols indicate undetectable values. Light grey bands are the interquartile range from standard HIV-1-infected individuals under treatment.

Figure 2

Genetic variability and evolutionary dynamics of viral populations (A) Phylogenetic trees with env gene sequences of the individuals during follow-up. The evolutionary history was inferred in trees by using the Maximum Likelihood method based on the General Time Reversible model. The percentage of trees in which the associated taxa clustered together with values over 70% is shown next to the branches. Initial tree for the heuristic search was obtained by applying the Neighbor-Joining method to a matrix of pairwise distances estimated using the Maximum Composite Likelihood approach. A discrete Gamma distribution was used to model evolutionary rate differences among sites (4 categories). The tree is drawn to scale, with branch lengths measured in the number of substitutions per site. Evolutionary analyses were conducted in MEGA6. Different colors were used to indicate the sampling time. (B) Genetic variability analysis of samples from different groups of HIV-1 individuals with a controlled infection (see Materials and Methods).

Figure 3

Cellular Immune responses. (A) Total CD8⁺ T-cell Gag-specific response from EEC and HIV-1-infected individuals on suppressive ART. (B) INDEX of polyfuncionality (pINDEX) of Gag-specific total CD8+ T-cells from EEC and HIV-1-infected individuals on suppressive ART based on the proportions of cells producing intracellular combinations of IFN-γ, TNF-α, IL-2. (C,D) Viral inhibition assay. Assay of the ex vivo ability of CD8⁺ T cells to inhibit superinfected autologous CD4⁺ T cells of the three individuals. The figure shows day 7 of an infection with a laboratory viral strain (C) HIV-1_NFN-NX (CRR5-tropic) and (D) HIV-1_NL4–3 (CXCR4-tropic). Percentage of inhibition of CD4⁺ vs CD4⁺:CD8⁺ T cells is indicated in each individual. (E) Total myeloid dendritic cell quantification, comparing EEC with HIV-1-infected individuals on ART and non-HIV-1-infected healthy donors (HD). (A,B and E) Differences between groups were determined by Mann-Whitney U test.

Figure 4

Inflammation biomarkers and antibody titers. (A–E) Different inflammatory markers were analyzed including (A) hsCPR, (B) β2-microglobulin, (C) D-dimer, (D) IL-6 and (E) sCD163. EEC individuals were compared with HIV-1-infected individuals on ART and non-HIV-1-infected healthy donors (HD). (F) Plasma antibody titers, expressed as the inverse of the final serum dilution with a positive signal, in two samples 14 to 19 years apart.