Extended Data Fig. 7. Reservoir quantification and composition subgroup analyses.

a–c, Subgroup reservoir analyses for bNAb Therapy group (n = 16) (a); bNAb Therapy group (plus NIH pt., n = 20) including 4 additional participants from a corresponding NIH/NIAID clinical trial (b). Left panels show the frequency of intact and defective proviral genomes per 10⁶ CD4+ T cells (log normalized) as determined by Q4PCR pre-therapy and post-therapy (24–26 weeks) for each respective subgroup. Open symbols represent lower limit of detection (defined as half of intact proviral frequency assuming 1 intact proviral genome/total number of analysed cells without target identification). Green and red horizontal bars depict the mean with SD of intact and defective proviral frequencies, respectively. Statistical significance was determined using two-tailed paired Student’s t-test. Right panels show longitudinal changes in relative representation of proviral subtypes in the respective bNAb Therapy subgroups. Depicted are the fractions of intact and defective proviral subtypes relative to total proviruses recovered from each participant at the indicated time point. Proviral subtypes: Intact, SV, Structural Variation; MIG, Missing Internal Gene; LTR, LTR defects; MSD, Major Splice Donor mutation; NF, Non-Functional. Only participants for whom at least one intact proviral genome was recovered are shown (bNAb Therapy group n = 14; bNAb Therapy group plus NIH pt. n = 17). Horizontal bars show median and interquartile range (IQR). Statistical significance was determined using two-tailed Wilcoxon matched-pairs signed rank test. c, Relative change in proviral frequencies between pre-therapy (T1) and post-therapy time points (T2) for intact (green) and defective (red) proviral frequencies in bNAb Therapy subgroups. Plotted values depict relative change with the black horizontal bars showing the median change. Statistical significance was determined using two-tailed Wilcoxon matched-pairs signed-rank test for matched comparisons within bNAb Therapy subgroups, respectively.