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Simple Epidemiological Dynamics Explain Phylogenetic Clustering of HIV from Patients with Recent Infection

Figure 2

Excess clustering and excess co-clustering of virus from patients with early/acute infections.

Left: The mean CD4 cell count (top) and frequency of ambiguous sites (bottom) versus the threshold TMRCA used to form clusters. Middle: The assortativity coefficient, a measure of similarity of co-clustered taxa, versus the treshold TMRCA used to form clusters. Assortativity of CD4 is at top, and frequency of ambiguous sites is bottom. Right: The size of each matrix element is proportional to number of co-clusterings between taxa categorized by CD4 (top, ) or quartile of frequency of ambiguous sites (bottom). The color represents the extent to which the count of co-clusterings exceeds the expectation if clusters were forming at random. The color scale (far right) shows strong assortativity within quartiles. The vertical red bar represents the threshold which was used to create clusters and the matrix derived from the set of clusters. This threshold corresponds to the maximum of the assortativity coefficient for the derived matrix.

Figure 2

doi: https://doi.org/10.1371/journal.pcbi.1002552.g002