Revealing the history of infectious disease epidemics through phylogenetic trees

Holmes EC, Nee S, Rambaut A, Garnett GP & Harvey PH

(1995) Phil Trans Roy Soc B 349, 33-40.

Phylogenetic trees play an increasing role in molecular epidemiology, where they have been used to understand the forces that shape patterns of viral sequence diversity. Phylogenetic trees can also be used to trace the dynamics of viral transmission within populations. Case studies document the worldwide spread of Human Immunodeficiency Virus type 1 (HIV-1) and hepatitis C virus (HCV). Despite similarities between these viruses, especially in their transmission routes, they are shown to have very different epidemiological histories. A possible reason for the difference is that HCV has coexisted longer with human populations.

Andrew Rambaut, 2007