Extended Data Figure 3: Phylogenies and Highlighter plots for the Pol region of HIV-1.

a–c, Maximum-likelihood trees were constructed using gene sequences from the Pol region (reverse transcriptase (Pol2)) of HIV-1 from lymph node and blood before and after the guanosines within all possible APOBEC3 trinucleotide sequence context of edited sites were masked in the alignments, regardless of their presence in hypermutated or non-hypermutated sequences, to avoid their distortion in the phylogenetic reconstructions. Branch tips are coloured according to compartment sampled: red for plasma; gold for lymph node; and blue for blood. The progressive shading of the colours of the branch tips indicate the points in time sampled. The horizontal scale indicates the expected number of substitutions per nucleotide site per unit time with haplotypes from later time points having diverged more. The Highlighter plots show the haplotypes from the lymphoid tissue and blood time point clusters aligned to the plasma virus sequence from day 0. The particular nucleotide changes are colour-coded in the alignment (thymidine, red; adenosine, green; cytosine, blue; and guanosine, orange). Magenta circles represent APOBEC3-induced G-to-A change in a trinucleotide context of the edited sites. Gene sequences from the Pol region of HIV-1 that spanned the genomic region encoding the viral enzyme reverse transcriptase from subjects 1774, 1727, and 1679 (a, b and c, respectively) before and after the guanosines within the particular APOBEC3 trinucleotide sequence context of edited sites were masked in the entire sequence alignment (left and right panels, respectively).