Differences in HIV-1 reservoir size, landscape characteristics, and decay dynamics in acute and chronic treated HIV-1 Clade C infection

Abstract

Persisting HIV reservoir viruses in resting CD4 T cells and other cellular subsets are a barrier to cure efforts. Early antiretroviral therapy (ART) enables post-treatment viral control in some cases, but mechanisms remain unclear. We hypothesised that ART initiated before peak viremia impacts HIV-1 subtype C reservoirs. We studied 35 women at high risk of infection from Durban, South Africa, identified with hyperacute HIV by twice-weekly HIV-RNA testing. Participants included 11 starting ART at a median of 456 (297-1203) days post-onset of viremia (DPOV) and 24 at 1 (1-3) DPOV. Peripheral blood mononuclear cells (PBMCs) were used to measured total HIV-1 DNA by droplet digital PCR (ddPCR) and sequence viral reservoir genomes by full-length proviral sequencing (FLIP-seq). ART during hyperacute infection blunted peak viremia (p<0.0001), but contemporaneous total HIV-1 DNA did not differ (p=0.104). Over 1 year, a decline of total HIV-1 DNA was observed in early treated persons (p=0.0004), but not late treated. Among 697 viral genome sequences, the proviral genetic landscape differed between untreated, late treated, and early treated groups. Intact genomes after 1 year were higher in untreated (31%) versus late treated (14%) and early treated (0%). Treatment in both late and early infection caused more rapid decay of intact (13% and 51% per month) versus defective (2% and 35%) viral genomes. However, intact genomes persisted 1 year post chronic treatment but were undetectable with early ART. Early ART also reduced phylogenetic diversity of intact genomes and limited cytotoxic T lymphocyte immune escape variants in the reservoir. Overall, ART initiated in hyperacute HIV-1 subtype C infection did not impact reservoir seeding but was associated with rapid intact viral genome decay, reduced genetic complexity, and limited immune escape, which may accelerate reservoir clearance in combination with other interventional strategies.

Keywords: Clade C; HIV-1; human; infectious disease; medicine; microbiology; reservoir; viral dynamics.

Figure 1.. Plasma viral load and total HIV DNA in acute treated and chronic treated individuals.

(A) Peak viral load (parametric t-test) and total HIV DNA (non-parametric t-test) measured at peak viral load in untreated (pre-therapy) and acute treated individuals. (B) Longitudinal viral load (Kruskal-Wallis ANOVA) (*1 viral load measurement was unavailable) and total HIV DNA (Kruskal-Wallis ANOVA) in untreated acute infection and after 6 and 12 months of treatment. (C) Longitudinal viral load (Kruskal-Wallis ANOVA) and total HIV DNA (non-parametric t-tests) in acute treated individuals. (D) Viral load and total HIV DNA (parametric t-test) after 1 year of treatment in chronic and acute treated individuals. Median and interquartile range (error bars) are represented.

Figure 2.. Genotypic characterisation of HIV-DNA sequences.

(A) Peripheral blood mononuclear cell (PBMC) sequencing time points in untreated (red), chronic treated (green), and early treated (blue) study participants where each dot represents a sampling time point. Time of treatment initiation is shown by the vertical grey bar. (B) Approximately maximum-likelihood phylogenetic tree of intact HIV-1 DNA genomes constructed using FastTree2. This method was chosen to resolve full-viral-genome sequences with extreme homology; branch lengths were likely inflated. Viral genomes derived from acute treated participants are marked with (*). (C) Comparison of intraparticipant mean pairwise distances between early and late treated participants. (D) Spectrum of HIV genome sequences detected during untreated acute infection, late treated chronic infection, and acute treated infection.

Figure 2—figure supplement 1.. In this cohort of HIV-1 subtype C, genome deletions were most frequently observed between integrase and envelope relative to Gag (p<0.0001–0.001).

Figure 3.. Evolution of the proviral genetic landscape.

Relative proportions of intact and defective viral genomes measured longitudinally in (A) untreated acute infection for 2 years, (B) late (chronic) treated infection for 1 year, and (C) early (acute) treated infection for 1 year. The number of genomes sampled at each time point is indicated above each vertical bar.

Figure 3—figure supplement 1.. Clonal expansion of infected cells was detected in both defective (orange) and intact (blue) genomes in late and early treated study participants.

This analysis was performed with all sequences available for each participant at all time points.

Figure 4.. Decay kinetics of intact and defective proviruses.

Absolute frequencies of intact and defective HIV-1 DNA sequences per million peripheral blood mononuclear cells (PBMCs) during the first year of infection following treatment during (A) acute infection and (B) chronic infection. Longitudinal analysis of the change in (C) intact and (D) defective provirus copies in the 6 months after antiretroviral therapy (ART) initiation, comparing the acute treated (blue) and chronic treated (green) groups. Dots represent a measurement from a given participant; solid lines are slopes estimated from linear mixed effect model. (E) Comparison of the monthly rate of decay of intact and defective proviruses in acute and chronic treated infection.

Figure 5.. Comparison of cytotoxic T lymphocytes (CTL) epitope diversity in late compared to early treated participants.

Proportion of participants with wildtype, variant, and CTL escape at baseline (within 1 month of infection) and up to 1 year of infection in Gag (A, D, G, J), Pol (B, E, H, K), and Nef (C, F, I, L) epitopes in participants with protective human leukocyte antigen (HLA) genotypes (A, B, C, G, H, I) and without protective HLA genotypes (D, E, F, J, K, L).