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. 2015 Mar:10:88-92.
doi: 10.1016/j.epidem.2014.09.001. Epub 2014 Sep 16.

Eight challenges in phylodynamic inference

Simon D W Frost  1 , Oliver G Pybus  2 , Julia R Gog  3 , Cecile Viboud  4 , Sebastian Bonhoeffer  5 , Trevor Bedford  6
Affiliations

Eight challenges in phylodynamic inference

Simon D W Frost et al. Epidemics. 2015 Mar.

Abstract

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.

Keywords: Coalescent models; Phylodynamics; Recombination; Selection.

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