Extended Data Fig. 10: Phylogenetic trees of gp160 env sequences from plasma.

Single genome sequencing-derived gp160 env sequences from the plasma of 9 RMs are displayed in maximum-likelihood phylogenetic trees. Virus obtained from different experimental phases are as follows: blue, SIVmac₂₃₉ inoculum; black, chronic infection prior to ART initiation (d52 p.i.); red, during on-ART ICB-mediated reactivation (d7-28 p.t.); and green, during acute rebound post-ATI. A scale bar indicating diversity for each phylogenetic tree is indicated below and lineage determinations are annotated for RUm16 (at right). Lineages were deemed distinct if they differed at 3 or more nucleotide positions over env.