FIG. 1.

Possible phylogenetic topologies relating three longitudinal sequences. The first sequence is taken at the initial time point, when R5 strains dominate the viral quasispecies (R5-p); the second sequence is taken at an intermediate time point when X4 strains are circulating (X4); and the third sequence is collected at the final time point, following initiation of potent new therapy and a concomitant suppression of X4 strains, resulting in a shift back to predominantly R5 strains (R5-r). The fourth sequence is an outgroup (O).