Fig. 2

Phylogenetic tree of the sequenced pol gene from the urine and blood viruses. The evolutionary history was inferred using the Neighbour-Joining method. The bootstrap values (1000 replicates) are shown next to the branches. The evolutionary distances were computed using the Kimura 2-parameter method. Evolutionary analyses were conducted in MEGA6. The sequence clusters from the 8 subjects with HIV-1 nucleic acid detected in urine are indicated. Red triangles—plasma RNA, blue squares—urine supernatant variants, empty blue squares—urine pellet variants. Sequences are named using time points (e.g. 6 M = 6 months, BL baseline)