Appendix Figure 4. Comparison of DNA distance estimations in
nine participants using Kimura 2-parameter (K2P) model of evolution with
a transition to transversion ratio of 2 (2)
vs. a General Time Reversible (GTR) model with a site-to-site variation
in substitution rates (discrete approximation of a 
distribution with a shape parameter, 
=0.5)
(5).
DNA distance estimates are shown for sequences from PBMC only in all participants
except for Participant1, where plasma data is shown for the time points
when PBMC samples were not available, and Participant 11 for whom insufficient
amounts of viral DNA was found in PBMC. K2P distances are plotted as blue
circles and GTR DNA distances are plotted as red triangles. Intra-time
point DNA diversity is depicted by open symbols and the DNA distance as
compared to founder sequences is shown by filled symbols. These comparisons
show similar trends using either K2P or the GTR distances, and as expected,
at high levels of DNA differences, GTR model yields a comparatively higher
DNA distances.