Transient viral replication during analytical treatment interruptions in SIV infected macaques can alter the rebound-competent viral reservoir
Fig 5
Frequency of rebounding lineages in CA-vDNA on ART reflects replication during ATIs.
The relative DNA frequencies of select lineages that rebounded in ATI-3 are tracked in vDNA on ART for animals H860, H814, and H34G. In panel (A), the grey points correspond to the cumulative peak viral loads of barcodes, rank-ordered based on their relative frequency at d10. The dark grey lines depict the pre-ART barcode distribution, with increases in total viral load highlighted by vertical line segments. Select lineages that were dominant in pre-ART plasma viremia but subsequently increased negligibly in total viral load are highlighted in red, while variants with over 10-fold higher level of replication during ATI-2 than primary infection are highlighted in blue. In panel (B), the red filled circles depict the relative frequencies of predominant barcodes in vDNA while the open circles indicate the limit of detection at time points when a particular barcode was not observed. The grey bars highlight the time intervals when the animals were off therapy, with the red bars indicating the relative frequency of the barcode at peak viremia during each interval. In panel (C), the blue filled circles depict the vDNA frequencies of the lineages that replicated substantially during ATI-2, while the open circles indicate the limit of detection at time points when a particular barcode was not observed. The grey bars again highlight the time intervals when the animals were off therapy, with the blue bars indicating the relative frequency of that barcode at peak viremia during each interval. The dashed lines indicate the relative frequency of each lineage based on cumulative peak plasma viral load.