Appendix Figure 2. Pairwise comparisons of virus population divergence
from the founder population (panels on the left side of the figure) and
diversity within each sample (panels on the right) in each of the nine
participants. Pairwise distances were estimated using the Kimura 2-parameter
model of viral evolution (2). These distances were
plotted on the y-axis at the corresponding times following seroconversion.
The lines within each panel connect the mean values for each time point.
Comparisons of sequences from PBMC are shown with a red open circle for
each data point, those from plasma are shown with a blue vertical line
for each data point. The first 5 panels show the estimates of viral diversification
for participants in which sequences were sampled from both PBMC and plasma.
Subsequent panels show these estimates sequences sampled from PBMC DNA or
from plasma RNA (but not both at any time point).