Clonal expansion dynamics on ART in individuals treated during acute and chronic infection.

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• Integration site analysis, near full-length proviral sequencing and phenotype analysis of p24 + cells. Maximum-likelihood phylogenetic trees for four Acute UD individuals. The trees include sequences with HXB2 coordinates 5089-9602. Naïve (TN), central/transitional memory (TCM/TTM), effector memory (TEM) and terminally differentiated (TTd) T cells are represented by triangles, rectangles, circles and diamonds, respectively. Proviral classification is color-coded. The integration sites are depicted and are color-coded according to their orientation to the host gene. (Peri-) centromeric DNA and KRAB-ZNF genes on chr19 are highlighted with a green and yellow frame, respectively. HXB2 subtype B is HIV-1 reference genome. NFL: near full-length.
  od: Tine Struyve (22683295)
  Izdano: (2025)
• Integration site analysis and near full-length (NFL) sequencing of p24 + cells. (A) Donut charts displaying the number of HIV integration sites (IS) obtained by ISLA from p24 + cells for four participants in the corresponding Fiebig group. White parts indicate IS detected once and colored parts indicate IS detected more than once. The total number of IS generated by ISLA for each participant is shown in the middle of each donut. (B) Proportion of intact and defective proviral sequences from p24 + cells (n = 47 sequences).
  od: Tine Struyve (22683295)
  Izdano: (2025)
• Frequencies and phenotypes of p24 + cells following PMA/Tat_LNP stimulation. (A-D) CD4 T cells from Acute UD, Acute UD + 5, Chronic UD and Chronic UD + x individuals were stimulated for 24h with PMA/Tat_LNP (A) Frequencies of p24 + cells in CD4 T cells. Median values are plotted. Open circles represent limit of detection (LOD). (B) Percentages of HIV-infected cells expressing the p24 protein following stimulation. Median values are plotted. Participants with an LOD frequency of p24 + cells in CD4 T cells or unreportable/unavailable total HIV DNA quantification were not included in this analysis. (C) Frequencies of cells with a given phenotype (TN, TCM/TTM, TEM, TTd) in p24+ and p24- fractions. Participants with a minimal number of 4 p24 + cells are represented. Grey bars depict median values. (D) Proportions of all p24 + cells with a given phenotype (TN, TCM/TTM, TEM, TTd). p24 + cells (
  od: Tine Struyve (22683295)
  Izdano: (2025)
• Integration site features of proviruses from Acute UD, Acute UD + 5 and Chronic UD individuals. (A) Pie charts displaying proportions of IS in genic regions with same, opposite and mixed orientation relative to the host gene. (B) Pie charts displaying proportions of IS in centromeric/satellite DNA, ZNF genes with KRAB domain on chr19, other genic regions and other non-genic regions. (C) Bar plots showing the proportions of IS in Hi-C compartments A1-A2 and B1-B4. Cumulative proportions of IS in compartments A and B are indicated on the left side of the graph. (D) Bar plots showing the proportions of IS in repetitive elements. Cumulative proportions of IS in repetitive elements are indicated on the left side of the graph. (E-F) Boxplots showing ChIP-Seq reads corresponding to activating (E) or inhibiting (F) histone features in linear proximity (+/-5 kb) of IS. (A-D) n represent the number of IS in the analysis. Chi-squared test (A) or Fisher’s exact test (B-
  od: Tine Struyve (22683295)
  Izdano: (2025)
• Schematic overview of participant sampling timeline.
  od: Tine Struyve (22683295)
  Izdano: (2025)