title: Unifying the epidemiological and evolutionary dynamics of pathogens.
abstract: 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.
authors.affiliation: Department of Zoology, University of Cambridge, Downing Street, Cambridge, CB2 3EJ, UK. btg11@cam.ac.uk
authors.forename: Bryan T
authors.initials: BT
authors.lastname: Grenfell
authors.forename: Oliver G
authors.initials: OG
authors.lastname: Pybus
authors.forename: Julia R
authors.initials: JR
authors.lastname: Gog
authors.forename: James L N
authors.initials: JL
authors.lastname: Wood
authors.forename: Janet M
authors.initials: JM
authors.lastname: Daly
authors.forename: Jenny A
authors.initials: JA
authors.lastname: Mumford
authors.forename: Edward C
authors.initials: EC
authors.lastname: Holmes
mesh_terms: D000222:Adaptation, Physiological; D000818:Animals; D000940:Antigenic Variation / Q000235:genetics; D005075:Biological Evolution; D004196:Disease Outbreaks / Q000662:veterinary; D005828:Genetics, Population; D006801:Humans; D007109:Immunity; D009154:Mutation; D010802:Phylogeny; D011157:Population Dynamics; D012327:RNA Virus Infections / Q000453:epidemiology* / Q000276:immunology / Q000662:veterinary / Q000821:virology*; D012328:RNA Viruses / Q000235:genetics* / Q000276:immunology / Q000472:pathogenicity* / Q000502:physiology; D012641:Selection, Genetic; D013997:Time Factors; D014611:Vaccination