Dynamic Correlation between Intrahost HIV-1 Quasispecies Evolution and Disease Progression
Figure 7
Evolutionary rate as a function of the distance from the root of the maximum likelihood tree of each patient.
(A) Maximum likelihood tree for the viral sequences sampled from patient S-P6 over 6 years [13]. (B) Evolutionary rate as a function of the distance from the root of the tree for 9 patients from Ref. [13] and 6 patients from Ref. [22] (black lines). The evolutionary rate between sequence i and j is estimated by the distance difference, dj−di, divided by the sampling time difference, tj−ti. The evolutionary rate at a certain distance from the root d was averaged over all possible sequence pairs (i, j) within a sliding window. The distance from the root for a particular window d ̅ is the average distance for all the sequences within that window. The size of the window (Δ) was 0.09 substitutions per site for S-P1 to S-P11 and 0.02 for W-P1 to W-P6. Error bars indicate ±1 standard deviation. The fitted rate of evolution with the full model to the divergence and diversity dynamics of each patient is depicted as blue line.