Characteristics of the study participants.

Correlation matrix of viral reservoir measures at 24 and 156 weeks after start of ART.

Correlation coefficients (rho) determined by Spearman correlation analyses are shown. Strength of positive and negative correlations is indicated by the color shade displayed in the legend. Significant correlations are indicated by *** if p<0.001 or by ** if p<0.01. All significant correlations remained significant after corrections for multiple comparisons.

Paired comparisons of viral reservoir measures at 24 and 156 weeks of ART.

Open symbols represent values below the detection limits of the assays. The four participants with a positive QVOA at 24 weeks are marked with colors (purple, blue, green, or red). Paired Wilcoxon test was performed to test the significance of the differences between the time points (* if p<0.05 or ** if p<0.01). Pairs where both values were undetectable, or where one was undetectable and its detection limit was higher than the value of the detectable partner, were excluded from the analysis. Exact p values are indicated below the graphs.

Correlations of reservoir measures and HIV-specific CD8+ T-cell responses as determined by IFN-γ release assay, AIM, and proliferation assay (proliferating cells and precursor cells).

The immune responses are defined as the sum of the responses to Env, Gag, Nef and Pol combined at 24 and 156 weeks. Correlation coefficients (rho) determined by Spearman correlation analyses are shown. Strength of positive and negative correlations is indicated by the color shade displayed in the legend. Significant correlations are indicated by *** if p<0.001 or by ** if p<0.01. All significant correlations remained significant after corrections for multiple comparisons.

Variables measured at 24 weeks ART associated with the changes in HIV-1 reservoir markers between 24 and 156 weeks of ART.

Overview of NOVA cohort study procedures for study groups 2 and 3.

ART, combination antiretroviral therapy; GALT, gut-associated lymphoid tissue; PBMC, peripheral blood mononuclear cells. Retrieved from: Dijkstra M. et al. Cohort profile: the Netherlands Cohort Study on Acute HIV infection (NOVA), a prospective cohort study of people with acute or early HIV infection who immediately initiate HIV treatment. BMJ Open. 2021;11(11):e048582.

A. Plasma viral load (pVL) B. CD4 T-cell count (×10^6/mL) and C. CD4/CD8 ratio at baseline, 24 weeks and 156 weeks post ART initiation. Participant X (green dot) had detectable loads of 200 and 100 cp/mL at 24 and 156 weeks. Participant Y (pink dot) had detectable loads of 74 and 98 cp/mL at 24 and 156 weeks. Lower limit of quantification of the assays used ranged between 40 copies (earlier) and 20 copies (later time points) (see Methods).

Comparison of intact HIV DNA levels at 24 weeks ART between participants with positive (n=6) and negative (n=14) QVOA.

Mann-Whitney test was used to determine statistical significance. *, 0.01<p<0.05.

Longitudinal analysis of frequencies of activated and naive, memory and effector subsets within the CD4+ (A) and CD8+ T-cell (B) populations.

Wilcoxon signed rank test (p<0.05) was used to determine statistical significance of the differences between the timepoints.

A. The frequency of dextramer+ CD8+ T-cells at 24 and 156 weeks after ART. B. The expression of exhaustion markers (upregulation of PD-1, CTLA-4, and CD160 expression; loss of CD28 expression) on HIV-dextramer specific CD8+ T-cells at 24 and 156 weeks after ART. For participants that were HLA-A*2 and HLA-B*7 positive, HLA-A*2 and HLA-B*7 dextramer staining was included separately. HLA-A*2 dextramer is marked as a triangle and HLA-B*7 dextramer as a square in both figures.

HIV-specific T-cell responses upon HIV-peptide stimulation (Env, Gag, Nef, Pol) at 24 and 156 weeks after ART.

IGRA/ IFN-γ release (A), AIM reactive CD8+ T-cells (B), precursor frequency (C) and the proportion of proliferating CD8+ T-cells (D). Frequencies of proliferating cells in response to Env, Gag, Nef and Pol peptides were combined. Overall, no significant difference in IGRA over time was observed.

Correlation matrix of reservoir measurements and the frequency of dextramer+ CD8+ T-cell responses at 24 and 156 weeks after ART initiation.

The correlation coefficient (rho) determined by Spearman correlation is shown. Positive and negative correlations (rho) are indicated by the color shade displayed in the legend. Significant correlations are indicated by * if p<0.05 or ** if p<0.01.