Fig. 2. Hypothetical coalescent scenarios depicting how the time between index case infection and time of stable coalescence can vary on the basis of stochastic extinction events of basal viral lineages.

Coalescence can occur within or contemporaneously with the index case (upper left) or, in cases infected later in the course of the epidemic, with one (upper right) or more (lower left) basal lineages going extinct. In extreme cases, the epidemic can persist at low levels for a long time before stable coalescence (lower right).