Epidemic Reconstruction in a Phylogenetics Framework: Transmission Trees as Partitions of the Node Set.

ABSTRACT: The use of genetic data to reconstruct the transmission tree of infectious disease epidemics and outbreaks has been the subject of an increasing number of studies, but previous approaches have usually either made assumptions that are not fully compatible with phylogenetic inference, or, where they have based inference on a phylogeny, have employed a procedure that requires this tree to be fixed. At the same time, the coalescent-based models of the pathogen population that are employed in the methods usually used for time-resolved phylogeny reconstruction are a considerable simplification of epidemic process, as they assume that pathogen lineages mix freely. Here, we contribute a new method that is simultaneously a phylogeny reconstruction method for isolates taken from an epidemic, and a p

SUBMITTER: Hall M 

PROVIDER: S-EPMC4701012 | biostudies-literature | 2015 Dec

REPOSITORIES: biostudies-literature