FIG. 3.

Neighbor-joining phylogenetic trees of pol single genome sequences. Neighbor-joining trees are shown of (A) all full-length single genome sequences—nucleotides 1893–3408, HXB2 numbering, (B) the 5′ end of all single genome sequences—nucleotides 1893–2390, and (C) the 3′ end of all single genome sequences—nucleotides 2590–3408. Depicted are single genome sequences of blood plasma RNA from 34 weeks (yellow triangles), 54 weeks (red circles), 85 weeks (blue squares), and 87 weeks (purple diamonds) postdiagnosis, and of seminal plasma RNA 87 weeks postdiagnosis (green upside down triangles). Hash tags (#) indicate sequences in CRF19 and subtype B clusters that were identified as CRF19/B recombinants by SimPlot (see the main text). Scale bars indicate genetic distance (amino acid substitutions per site). Asterisks (*) indicate that clustering of CRF19, subtype B, and recombinants is supported by bootstrap values of >75%. Color images available online at www.liebertpub.com/aid