FIG. 5.

Highly heterogeneous, multiple variant env sequence populations are visually represented by phylogenetic trees with extensive branch structure and discernible clades (left) and Highlighter plots with diverse patterns of nucleotide base mutations compared to the intraparticipant consensus (right). env variants resulting from recombination between clades are displayed below with RAP (for recombination analysis program) plots. Parental strains for each recombinant are color coded on the trees, with regions within each recombinant likewise color coded to correspond to respective parental strains. Recombination breakpoints are illustrated by empty boxes on RAP plots. (A) Participant CAP37 was infected with three distinct variants. Sequence 5998 differs by up to 6% from the remaining sequences from this participant and is a suspected dual infection. (B) Participant CAP69 was infected with at least five distinct viruses with extensive recombination between clades. Six recombinant strains are illustrated here.