Figure 4.

Characteristics of single transmitted HIV-1 Variants. Aligned haplotypes derived from NGS env nucleotide sequences for linked sources (blue and red triangle representing sequences derived from seminal and blood plasma RNA respectively) and recipients (green triangle) were used to generate ML trees for individual transmission pairs. Bootstrap support values are indicated. Distribution and ranking position of the transmitted (red) and not transmitted (blue) haplotypes are indicated for each source. Single transmitted founder variants were defined by a maximum pairwise diversity of <0.10 substitutions/site and a monophyletic clade visualized on the tree topology with a minimum bootstrap support of 70 percent. * The most closely related (transmitted) source variant haplotype to the recipient viral population.