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The field of phylodynamics, which attempts to enhance our understanding of infectious disease dynamics using pathogen phylogenies, has made great strides in the past decade. Basic epidemiological and evolutionary models are now well characterized with inferential frameworks in place. However, significant challenges remain in extending phylodynamic inference to more complex systems. These challenges include accounting for evolutionary complexities such as changing mutation rates, selection, reassortment, and recombination, as well as epidemiological complexities such as stochastic population dynamics, host population structure, and different patterns at the within-host and between-host scales. An additional challenge exists in making efficient inferences from an ever increasing corpus of sequence data.

Original publication

DOI

10.1016/j.epidem.2014.09.001

Type

Journal article

Journal

Epidemics

Publication Date

03/2015

Volume

10

Pages

88 - 92

Keywords

Coalescent models, Phylodynamics, Recombination, Selection, Biological Evolution, Communicable Diseases, Genetic Variation, Host-Pathogen Interactions, Humans, Models, Statistical, Phylogeny, Population Dynamics, Recombination, Genetic, Selection, Genetic, Stochastic Processes