Inference of Transmission Network Structure from HIV Phylogenetic Trees.

ABSTRACT: Phylogenetic inference is an attractive means to reconstruct transmission histories and epidemics. However, there is not a perfect correspondence between transmission history and virus phylogeny. Both node height and topological differences may occur, depending on the interaction between within-host evolutionary dynamics and between-host transmission patterns. To investigate these interactions, we added a within-host evolutionary model in epidemiological simulations and examined if the resulting phylogeny could recover different types of contact networks. To further improve realism, we also introduced patient-specific differences in infectivity across disease stages, and on the epidemic level we considered incomplete sampling and the age of the epidemic. Second, we implemented an inference

SUBMITTER: Giardina F 

PROVIDER: S-EPMC5279806 | biostudies-literature | 2017 Jan

REPOSITORIES: biostudies-literature