A key priority for infectious disease research is to clarify how pathogen genetic variation, modulated by host immunity, transmission bottlenecks, and epidemic dynamics, determines the wide variety of pathogen phylogenies observed at scales that range from individual host to population. We call the melding of immunodynamics, epidemiology, and evolutionary biology required to achieve this synthesis pathogen "phylodynamics." We introduce a phylodynamic framework for the dissection of dynamic forces that determine the diversity of epidemiological and phylogenetic patterns observed in RNA viruses of vertebrates. A central pillar of this model is the Evolutionary Infectivity Profile, which captures the relationship between immune selection and pathogen transmission.

Original publication

DOI

10.1126/science.1090727

Type

Journal article

Journal

Science

Publication Date

16/01/2004

Volume

303

Pages

327 - 332

Keywords

Adaptation, Physiological, Animals, Antigenic Variation, Biological Evolution, Disease Outbreaks, Genetics, Population, Humans, Immunity, Mutation, Phylogeny, Population Dynamics, RNA Virus Infections, RNA Viruses, Selection, Genetic, Time Factors, Vaccination