FIG. 2.

Mosaic structure of env genes. The full-length env sequences from the surgeon and his patient were analyzed after alignment with reference subtype HIV-1 sequences. Phylogenetic trees were constructed from sequential 250-bp segments overlapping by 20 bp. The bootstrap values from 1,000 replicates, indicating grouping with subtypes A (thick solid line), F (thin solid line), and C (dashed line), are plotted. The results from two analyses obtained with one sequence from each patient (FRCNP5 and FRMNR2) are shown and are representative of results obtained with the other sequences. Other bootscanning analyses were also performed with other reference and outgroup sequences (data not shown), and the segments of subtype C-related material were not consistently found (data not shown). Recombination breakpoints were identified at the intersection of the lines from the plots.