Simple Epidemiological Dynamics Explain Phylogenetic Clustering of HIV from Patients with Recent Infection
Dark branches with taxa labeled A correspond to stage-1 (early/acute infected hosts). Light branches with taxa labeled C correspond to stage-2 (chronic infections). Event 1 represents the coalescence of two lineages corresponding to early/acute infection. Event 2 represents coalescence of an early and a late infection. Event 3 represents the stage transition of an early infection to a late infection. Event 4 represents the transmission by a late infection which is not ancestral to the sample. Top: Includes an unsampled lineage (dashed). Middle: The unsampled lineage has been pruned from the tree. The point where the lineage is pruned corresponds to event 4. Bottom: The number of lineages as a function of time (NLFT) which correspond to a host with early/acute infection (black) or chronic infection (grey).