Fig. 4.

Detection of HIV superinfection in the p24 region. Neighbor-joining trees of HIV p24 next-generation consensus sequences (≥10 identical reads) from female_C1 (green) in 2002 (A) and 2005 (B) are shown. The trees were constructed with a selection of subtype reference sequences and random sequences from individuals in Rakai shown in black. Superinfecting strains are shown with a circle. Brackets demonstrate the individual's HIV subtypes within the trees. Bootstrap values higher than 80% are shown (1,000 replicates).