Figure 2. Elimination of recipient-derived CD4⁺ T cells after alloHSCT results in profound decreases in cell-associated SIV DNA across blood and tissue reservoirs.

(A-D) Cell-associated SIV DNA in blood and tissues from alloHSCT recipients (colored bars) and time-matched controls (black bars) from Figure 1. Black dotted horizontal lines indicate the LOQ for SIV DNA (13 copies/million cells). Bars not shown represent undetectable SIV DNA copies. Asterisks (*) indicate measurements not performed due to technical issues. (E) Correlation of CD4⁺ cell-associated SIV DNA copy number and CD4⁺ donor chimerism in blood and tissues sampled from the HSCT recipients shown in A. Symbol colors and shapes correspond to a particular recipient (see A-D) and tissue, respectively. Undetectable SIV DNA were considered 0 for this analysis. r and p-values calculated by Spearman test: *p ≤ 0.05, ** p ≤ 0.01, ***p ≤ 0.001, ****p ≤ 0.0001. PeriphLN = peripheral (axillary/inguinal) lymph nodes, MesLN = mesenteric lymph nodes, BM = bone marrow. (F) Study outline for alloHSCT macaques (n=4) euthanized post-HSCT during ART treatment. RIC = reduced intensity conditioning. (G) Longitudinal SIVmac239 plasma viral loads from infection until euthanasia. Colored dotted vertical lines indicate the day of HSCT for each HSCT recipient. Black dotted horizontal line indicates the LOQ (50 copies/mL). Undetectable values are graphed at the LOQ. Macaques were maintained on daily ART from the indicated initiation timepoint until euthanasia. (H) Correlation of CD4⁺ T cell-associated SIV DNA copy number and CD4⁺ T cell donor chimerism in blood and tissues sampled from the recipients shown in F and G. Symbol colors and shapes correspond to a particular recipient macaque and tissue (see part E legend), respectively. r and p-values calculated by Spearman test using log-transformed SIV DNA copies: *p ≤ 0.05, ** p ≤ 0.01, ***p ≤ 0.001, ****p ≤ 0.0001. Undetectable SIV DNA were considered 1 for this analysis. See also figures S1, S2, S4.