Fig. 1

Evolution of within-host nef sequences. a Participant plasma viral load (solid blue line), CD4+ T-cell count (red dotted line) and sampling history (colored circles). Grey shading indicates periods on cART. b Maximum likelihood phylogenetic tree inferred from 50 unique within-host nef sequences, where the root represents the inferred most recent common ancestor (MRCA). Scale in estimated substitutions per nucleotide site. c Within-host Nef amino acid alignment, with sequences ordered according to the phylogeny, where the top sequence denotes the master and colored lines in the below sequences represent nonsynonymous substitutions with respect to it. Tickmarks on the X-axis are placed every 20 amino acids. d Linear relationship relating root-to-tip phylogenetic distances to sampling time; this analysis quantifies within-host HIV sequence divergence from the root over time. e Linear relationship relating average tip-to-tip phylogenetic distances between clonal sequences sampled each year to sampling time; this analysis quantifies within-host HIV sequence diversity over time. Colored dots represent the mean tip-to-tip phylogenetic distance and error bars show standard deviation