Simple Epidemiological Dynamics Explain Phylogenetic Clustering of HIV from Patients with Recent Infection
The x-axis gives the time since the beginning of the epidemic, or equivalently, the threshold TMRCA used to calculate the number of lineages over time. Green describes the simulated number of late infections. Blue describes the simulated number of early infections. Dots show the simulated ancestor function for the number of lineages that correspond to late infections. And x's show the simulated ancestor function for lineages in early infection. Dashed lines show the prediction of the deterministic coalescent. The top row shows results for a sample taken at 15 years following the initial infections, and the bottom shows results for a sample at 30 years. The right column shows results for a sample fractions of 20%, and the left column for a census of prevalent infections(100%).