Persistence of V3 variants in PBMC for S1. A. Time line with rainbow colors indicate timing of samples (black dots for clonal sequences; black dot with P for pyrosequences), as well as CD4% (black line) and log10 plasma viral levels (orange line), relative to age/length of infection in years. B. ML tree of longitudinal clonal V3 sequences resembled the topology of trees developed from Env V1 through V3 clonal sequences (sequence number: red – 19, yellow – 37, green – 7, blue - 13). Symbols: ovals, plasma RNA sequences; rectangles, cell-associated DNA sequences. Size of symbols represents relative abundance of sequences in the population. Colors represent time line of samples. Asterisks on a branch represent significant approximate likelihood-ratio test (* > 0.75, ** >0.90). Scale indicates 0.02 nucleotide substitutions per site. C. ML tree combining longitudinal conventional and single-time point deep sequences. Black symbols represent pyrosequences clustered at 3% pairwise distance with symbol shapes indicating proportion of sequences in each cluster: empty circle ≤ 0.25%; black inverted triangle, > 0.25% to 1%; black square, > 1% to 10%; star, > 10%. Brackets indicate colocalization of cell-associated viral variants by pyrosequencing with: “a”, clonal RNA and DNA viral sequences from earlier time point; or “b”, clonal plasma viral variants from later time points. Scale indicates 0.02 nucleotide substitutions per site.