Fig. 1: Barcoded full-length R5 tropic HIV-1 forms a reservoir and reveals stable genetic diversity of proviral lineages.
a Schematic showing cloning approach of the insertion of a 21 nt genetic barcode tag (red) constrained by a cytosine every third nt inserted downstream of env in a full length R5-tropic HIV-1 isolate NFNSX31. b Schematic representation of experiment; early infection of TKO-BLT mice with NFNSX-BC for 6 weeks, ART for 6 weeks, then ART interruption, followed by 6 weeks of monitoring for rebound infection. The red arrows denote when animals were sacrificed during early infection, ART suppression, and rebound infection. c Longitudinal plasma HIV RNA loads of groups of animals that were sacrificed after early infection, ART suppression, or rebound infection. Gray shading indicates an ART treatment period. The black dashed line indicates the detection limit of 2.3 log RNA copies per ml. Median ± interquartile range. d, e Number of viral RNA (vRNA) barcodes (BC) by timepoint. n represents the number of organs (d) or mice (e). f, g Shannon’s diversity (f) and Simpson’s dominance index (g) of vRNA BC by timepoint. n represents the number of organs. h, i Number of proviral BC by timepoint. Horizontal bars represent medians. n represents the number of organs (h) or mice (i). j, k Shannon’s diversity (j) and Simpson’s dominance index (k) of proviral BC by timepoint. n represents the number of organs. Horizontal bars represent mean values (d–g, j, k). n.s., p > 0.05. P values were calculated using the two-tailed Mann-Whitney test (d–k). Source Data c–k.
