Comparisons of the circulating latent reservoir and rebound viruses.

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Comparisons of the circulating latent reservoir and rebound viruses. Comparisons of the circulating latent reservoir and rebound viruses. (A) Diagrams show the overlap between env sequences obtained from Q2VOA (blue), NFL sequencing (yellow), and rebound plasma SGA or PBMC outgrowth culture (red) (17). The intersection of the NFL and Q2VOA circles represents the number of identical env sequences belonging to clones obtained by both methods. Sequences obtained from the preinfusion and week 12 were combined. (B) Maximum likelihood phylogenetic trees of env sequences obtained from Q2VOA at preinfusion (green) and week 12 (blue), NFL at the preinfusion (purple) and week 12 (orange), and rebound viruses from SGA or outgrowth cultures (red) from two representative participants. Additional participants are shown in SI Appendix, Fig. S4. (C) Circos plots depicting recombination events between env sequences derived from Q2VOA at preinfusion (blue), intact NFL at preinfusion (green), and rebound plasma SGA (red). Gray lines show the contribution of parent sequences to recombinant sequences. Clonal env sequences were collapsed and represented as one virus. The thickness of the black outer bars represents the number of sequences obtained from that particular clone. Asterisks indicate the same env sequences between intact NFL and Q2VOA sequences. Ching-Lan Lu et al. PNAS 2018;115:48:E11341-E11348 ©2018 by National Academy of Sciences