Fig. 2: Intraindividual HIV diversity can lead to reservoir underestimation by IPDA.

a Env gp120 amino acid and IPDA env probe nucleotide sequences from participant 91C33 identified by GenBank accession numbers. 91C33 harbored one HIV subpopulation that matched the IPDA env probe and was sensitive to bNAbs 3BNC117 and 10-1074, and another that harbored a mismatch at position 4 of the IPDA env probe and was resistant to both bNAbs. Hyphens (-) indicate matches to the reference; red letters denote mismatches (IPDA env probe) or amino acid substitutions (bNAb). Sequence is abbreviated seq. b ddPCR env plots from one of 2 independent experiments assessing the ability of the IPDA env reaction to detect representative within-host sequences MH632945 (env probe match) and MH632950 (env probe mismatch), present as purified env PCR products of equal length and comparable quantities. Positive droplets are green and negative droplets are grey. See Supplementary Fig. 3 for additional experiments. c Virus 3, isolated from participant OM5346’s reservoir, was sensitive to 10-1074-mediated ADCC but resistant to 3BNC117; vice-versa for virus 4. Box and error bars indicate mean and standard deviation of three technical replicates, from one of two independent experiments. Open circles denote individual datapoints. Source data are provided in the Source Data File. d 1D IPDA env ddPCR plots from one of 2 independent experiments for cells infected in vitro with virus 3 (IPDA env probe match) or virus 4 (G13A mismatch). Both viruses were detectable using an alternative primer/probe set (Supplementary Fig. 6). e Possible impacts of intraindividual HIV diversity on IPDA-measured reservoir changes following a hypothetical intervention. The solid line indicates the observed effect by IPDA; dashed line indicates the true effect. An intervention’s impact on the reservoir could be overestimated when a subset of within-host HIV sequences are undetectable by IPDA and resistant to treatment (e.g., 91C33 during treatment with 3BNC117 or 10-1074, or OM5346 during treatment with 10-1074). Conversely, an intervention’s impact on the reservoir could be underestimated when a subset of within-host HIV sequences are undetectable by IPDA and sensitive to treatment (e.g., OM5346 during treatment with 3BNC117). In a worst-case scenario, one could erroneously conclude that the treatment had no effect.