Fig. 3: Diversity of plasma viral RNA sequences prior to ART initiation.

a Phylogenetic tree of env sequences from plasma viral RNA in viremic, chronically SIV-infected monkeys at 14 weeks prior to initiation of ART. The black lines represent the SIVmac251 challenge stock and viral RNA sequences from each animal are shown in colors. b Average phylogenetic distance of plasma virus from each animal (n = 16) to the SIVmac251 challenge stock. c Average pairwise distance of virus population diversity for each animal (n = 16). b and c Viral divergence and viral diversity within each animal were compared to previously reported values of HIV-1-infected individuals after 1 year of infection14. Red horizontal bars indicate median values.