Fig. 3.

Phylogenetic trees corresponding to regions of differential homology in intercompartment mosaic E21BrD107. Patient E21's env alignment was divided into four segments, in agreement with the three breakpoints identified in isolate E21BrD107, and ML phylogenetic trees were constructed for each segment: positions 1 to 262 (A), positions 263 to 774 (B), positions 775 to 1514 (C), and positions 1515 to 2571 (D). Highlighted isolate E21BrD107 exhibits significant positional shifting between compartment specific clades.