Figure 2.

Neighbor-joining phylogenetic tree and Highlighter plot analysis of pol sequences. A, Neighbor-joining phylogeny of single-genome sequencing (SGS)–derived pol sequences from the chronically infected source patient's plasma viral RNA, displaying long branch lengths, with the exception of the single cluster of closely related sequences. Such sequence clusters of near identity have been reported as minor components of chronically infected patients' plasma virus quasispecies and reflect recent clonal expansion of a virus within a diverse chronic virus swarm [7]. B, Neighbor-joining phylogeny of SGS-derived pol sequences from the acutely infected index subject's plasma viral RNA reveals multiple low diversity lineages (variants 1–15; blue), as well as interspersed interlineage recombinant sequences (orange). C, A Highlighter plot of index case pol sequences represents as colored tics the nucleotide polymorphisms between the top sequence (43715D4) and the remaining pol sequences aligned below. The plot illustrates the homology of each of the T/F lineages (blue), the heterogeneity between T/F lineages, and the chimeric structure of the recombinant sequences (orange).