Genes, trees and infections: Molecular evidence in epidemiology.

Molecular phylogenies constitute an important new way of tracking the progress of viral epidemics. The phylogenetic analysis of viral sequence data provides information on the origin, spread and maintenance of infections and can be used to reconstruct contact networks of infected individuals. Analysis of the branching structure of phylogenetic trees also allows inferences to be made about the rate of transmission and the distinction between endemic and epidemic infections, and provides estimates of the numbers of infected individuals.