Fig. 1. Landscape of SIV genomes persisting in treated macaques is dominated by defective sequences.
(a) Time line of infection, treatment and sampling. Animals were infected with SIVmac251 for 95 weeks (red) before ART (blue box). All animals achieved and maintained suppression of viremia to <50 copies/ml of SIV RNA by week 20 of ART (dark blue box). Small arrows indicate sampling times. Samples for near full genome sequencing were obtained 36 weeks after ART initiation (red arrow). (b) Method for near full length, single genome analysis. Positions of PCR amplicons are shown in relation to a map of the SIV genome (top). See Methods for details, (c) Individual genomes from treated animals. Each horizontal bar represents a single genome. 221 genomes for which >1 inner PCR reaction was positive are shown. An additional 46 genomes were detected by near full genome length outer and nested gag inner PCR, but could not be fully sequenced due to large unmapped deletions (n=32) and/or extensive hypermutation (n=14). (d) Number of genomes with the indicated types of defects in each animal, (e) Comparison of 267 SIV sequences from 7 animals and 152 previously published (Bruner et al., 2016) HIV-1 proviral sequences from 10 individuals initiating ART during chronic infection. Significant differences between SIV and HIV-1 in the fraction of different categories of genomes are indicated (**, P < 0.01; ****, P < 0.0001). (f) Comparison of the average time periods of infection and ART between the SIV-infected macaques studied here and HIV-1-infected patients analyzed by Bruner et al., 2016.