Fig. 4. Reservoir quantification and composition.

a, Frequency of intact and defective proviral genomes per 10⁶ CD4⁺ T cells (log normalized) as determined by Q4PCR pre-therapy and post-therapy (26 weeks) for bNAb therapy with participants who have been on ART for at least 7 years (top, circles) and baseline and follow-up (24–58 weeks) for ART-alone (bottom, squares) groups, respectively. All participants with paired reservoirs measurements were included (bNAb therapy with at least 7 years ART n = 12, ART alone n = 10). Open symbols represent lower limit of detection (defined as half of intact proviral frequency assuming one intact proviral genome in the total number of analysed cells without target identification). Green and red horizontal bars depict mean ± s.d. of intact and defective proviral frequencies, respectively. b, Longitudinal changes in relative representation of proviral subtypes in the bNAb therapy with at least 7 years ART (top) and ART-alone (bottom) groups, respectively. 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; and NF, non-functional. Participants in whom at least one intact proviral genome was recovered are shown (bNAb therapy with at least 7 years ART n = 11, ART alone n = 9). Horizontal bars show median and interquartile range. c, Relative change in proviral frequencies (indicated at the bottom of each dataset) between pre-therapy (T1) and post-therapy time points (T2) for intact (green) and defective (red) proviral frequencies in bNAb therapy (circles) and ART-alone (squares) groups, respectively. Horizontal bars indicate median change. Open square with cross represents individual data point outside the y-axis range (relative change TSC − 127 = 0.09). P-values are shown at the top of graphs and were determined using two-tailed paired Student’s t-test in a and two-tailed Wilcoxon matched-pairs signed-rank test in b, c.