Fig. 2

Comparative analysis of UIS clonality in Acute-ART group vs. AIDS-ART group. a Pie chart analysis of monoclonal UIS proportions. The pie chart compares the proportion of monoclonal UIS in PLWH who initiated ART during the acute phase (n = 54) versus those who began treatment during the AIDS stage (n = 36). Colored bands around the outer edge of the pie chart represent the percentage of PLWH with personal monoclonal UIS counts >70% (blue), 50% (green), and 40% (yellow), respectively. Significant differences between groups are indicated by P-values by Chi-square test (P = 0.1205 for 70%, P = 0.0257 for 50%, P = 0.0013 for 40%). b Mosaic chart of UIS distribution. This mosaic chart shows the relative percentages of the top 5000 UIS in two groups: the Acute-ART group (left, n = 54) and the AIDS-ART group (right, n = 36). Larger blocks indicate greater homogeneity in clonal distribution patterns, while a higher number of smaller blocks represents a greater prevalence of monoclonal UIS within the group, and vice versa. c PMD analysis. This method assesses UIS clonality based on two dimensions: Richness (variety of UIS) and Evenness (distribution uniformity). The panel categorizes UIS as polyclonal or monoclonal, with the AIDS-ART group (middle) exhibits greater monoclonality, while the Acute-ART group (right) showing higher evenness. d Comparative analysis of PMD analysis in Acute-ART group vs. AIDS-ART group. The plot compares the evenness, richness, and PMD data between PLWH initiating ART during the acute stage (red dot) versus those during the AIDS stage (blue dot). e Longitudinal analysis of individual Top1 UIS percentage. This panel presents the percentage of the top 1 UIS counts for PLWH initiating ART during the acute stage (left panel) versus those during the AIDS stage (right panel). The X-axis represents different ART treatment time periods, and the Y-axis shows the top 1 UIS percentage. The gray line indicates the trend, with the gray shaded area representing the 95% confidence interval (CI). f Clustering of monoclonal UIS by Evenness, Richness, and ART duration. Patients are clustered based on Evenness and Richness data, with ART duration factored into the analysis. Monoclonal individuals in the AIDS group are shown in blue, while those in the acute group are shown in red. The black dashed line represents the 12 month mark. The bubble sizes represent for the UIS counts. The lager bubble represent for more UIS counts. g Cumulative curve of individuals percentage with monoclonal UIS during ART duration. The cumulative curve (left) displays the percentage of individuals with monoclonal UIS over time in the Acute-ART group (red line) versus AIDS-ART group (blue line). The curve shows a rapid increase in the percentage of PLWH initiating ART during the acute stage with monoclonal UIS within the first 12 months, followed by a more moderate rise. In contrast, PLWH initiating ART during the AIDS stage experience a substantial and immediate increase, reaching nearly 78% after 180 months. The bar chart (right) indicates the PLWH’ percentage with monoclonal UIS during different ART time periods, with red bars representing PLWH who initiated ART during the acute stage and blue bars representing those who started ART during the AIDS stage. h Schematic representation of proviral integration dynamics. The upper panel illustrates the dynamics of proviral integration across different stages of HIV infection, emphasizing the high rate of new integration events and the expansion of the latent reservoir. The diagram traces the progression from initial infection to detectable clonal expansion, where most newly infected cells perish, but a subset forms detectable clones. During the acute phase, there is increased diversity in provirus-integrated cells and UIS clones. Monoclonal UIS and cell clonality peak towards the end of the acute phase and then decline during the chronic infection stage, accompanied by a loss of HIV-integrated CD4 + T cells, as shown by the black trend line. In the AIDS stage, monoclonal UIS and cell clonality continue to accumulate. The middle panel demonstrates that initiating ART during the acute phase reduces the overall size of the latent reservoir and delays monoclonal UIS accumulation, leading to fewer integration site clones, as indicated by the red trend line. The lower panel shows that PLWH initiating ART during the AIDS stage have a larger latent reservoir and a higher prevalence of monoclonal UIS, along with increased homogeneity of monoclonal integration sites, as indicated by the blue trend line. The image was created using Biorender (https://biorender.com/). (Note: Distinct dots represented as each measurement in each bar chart and data are represented as mean ± SEM; p < 0.05 indicates statistical significance; Wilcoxon test for d; random linear regression test for g; the terms ‘Acute’ and ‘AIDS’ in all figures refer to PLWH who initiated ART during the acute stage (also referred to as the Acute-ART group) and those who initiated ART during the AIDS stage (also referred to as the AIDS-ART group), respectively)