Extremely low viral reservoir in treated chronically HIV-1-infected individuals

Abstract

Background: Small viral reservoirs are found predominantly in HIV-1 controllers and individuals treated during acute/early HIV-1 infection. However, other HIV⁺ individuals could naturally also harbour low viral reservoirs.

Methods: We screened 451 HIV-1-infected treated-individuals with suppressed plasma viremia for at least 3 years and stored cryopreserved peripheral blood mononuclear cells (PBMCs). Total HIV-DNA was analysed in PBMCs with ddPCR. Individuals with <50 HIV-DNA copies/10⁶ PBMCs constitute the 'Low Viral Reservoir Treated' cohort (LoViReT). Longitudinal samples were obtained from 12 chronically treated LoViReT and compared to 13 controls (>50 HIV-DNA copies/10⁶ PBMCs) to analyse total HIV-DNA, T-cell and NK-cell populations, HIV-1 specific antibodies, and plasma inflammation markers.

Findings: We found that 9.3% of the individuals screened had <50 HIV-DNA copies/10⁶ PBMCs. At least 66% initiated cART during the chronic phase of HIV-1 infection (cp-LoViReT). Cp-LoViReT harboured lower levels of HIV-DNA before cART and after treatment introduction the decays were greater compared to controls. They displayed a marked decline in quantity and avidity in HIV-specific antibodies after initiation of cART. Cp-LoViReT had fewer CD8⁺ T_TM and T_EMRA in the absence of cART, and higher CD8⁺ T_N after 18 months on therapy.

Interpretation: Treated chronically HIV-1-infected LoViReT represent a new phenotype of individuals characterized by an intrinsically reduced viral reservoir, less impaired CD8⁺ T-cell compartment before cART, and low circulating HIV-1 antigens despite being treated in the chronic phase of infection. The identification of this unique group of individuals is of great interest for the design of future eradication studies.

Funding: MSD Spain.

Keywords: HIV latency; HIV reservoir; HIV-specific antibodies; immunophenotyping; total HIV-DNA.

Fig. 1

Total HIV-1 DNA. (a) Total HIV-1 DNA of 451 individuals after screening with ddPCR. Subjects with <50 copies/10⁶ PBMCs are shown in light blue. (b) Comparative distribution of total HIV-1 DNA between the 2 recruiting centres. Subjects with <50 copies/10⁶ PBMCs are shown in blue and red respectively to the each site. (For interpretation of the references to color in this figure legend, the reader is referred to the web version of this article.).

Fig. 2

Longitudinal measure of total HIV-1 DNA in CD4⁺ T cells by ddPCR. (a) Decay in total HIV-1 DNA before and after initiation of cART. The light grey box indicates the period under cART. (b) Box plot of total HIV-1 DNA at 3 different time points: pre-cART, 18 months after initiation of cART, and 5 years after initiation of cART. (c) Fold change decay in the sample before initiation of treatment and after 5 years of cART. (d) Spearman correlation for total HIV-1 DNA pre-cART and after 5 years of cART.

Fig. 3

Analysis of maturation subsets, activation, exhaustion, and surrogate markers in the reservoir in CD8⁺ T cells. (a) Median CD8⁺ T-cell values for the frequency of the maturation subsets (naïve, central memory, effector memory, transitional memory, and effector memory RA⁺) in controls and cp-LoViReT at 3 different time points: pre-cART, 18 months after initiation of cART, and 5 years after initiation of cART. Maturation stages were defined based on the combination of CD45RA, CD197 (CCR7), and CD27. (b) CD45RA⁺CD197⁺ (Naive), (c) CD45RA^–CD197⁺ (central memory), (d) CD45RA^–CD197^–CD27^– (transitional memory), (e) CD45RA^–CD197^–CD27⁺ (effector memory), and (f) CD45RA⁺CD197^– (effector memory RA⁺). (g) CD8 activation levels (HLA-DR⁺CD38⁺) in both study groups over time. (h-j) CD8⁺ T-cell exhaustion markers including PD-1 (CD279), TIM-3, and LAG-3. The cp-LoViReT group is depicted in blue and the control group in grey. Intragroup statistically significant differences are depicted with a light blue or grey line for LoViReT and controls respectively; statistically significant differences between groups are depicted with a red line.

Fig. 4

CD4⁺ T cell susceptibility to HIV and viral inhibition by CD8⁺ T and NK cells. PBMC samples before initiation of cART and after 5 years on cART were used to analyse the susceptibility of CD4⁺ T cells to HIV BaL (CCR5 tropic strain) (10 ng p24/ml) (a). We also measured the ex vivo ability of CD8⁺ T cells (b) and NK cells (c) to inhibit superinfected autologous CD4⁺ T cells at a 1:1 ratio. The cp-LoViReT group is depicted in blue and the control group in grey.

Fig. 5

Measurement of HIV-1-specific antibodies. Plasma samples before initiation of cART and after 5 years of cART were tested for HIV-1-specific antibody levels using a detuned version of the HIV-1 VITROS assay (a) and a limiting antigen avidity assay (b). The dotted line represents the HIV-1 antibody assay diagnostic cut-off level used to classify individuals as HIV-1-positive or -negative. The p-values between groups were assessed using the Mann-Whitney test.