Detection of HIV transmission clusters from phylogenetic trees using a multi-state birth-death model.

ABSTRACT: HIV patients form clusters in HIV transmission networks. Accurate identification of these transmission clusters is essential to effectively target public health interventions. One reason for clustering is that the underlying contact network contains many local communities. We present a new maximum-likelihood method for identifying transmission clusters caused by community structure, based on phylogenetic trees. The method employs a multi-state birth-death (MSBD) model which detects changes in transmission rate, which are interpreted as the introduction of the epidemic into a new susceptible community, i.e. the formation of a new cluster. We show that the MSBD method is able to reliably infer the clusters and the transmission parameters from a pathogen phylogeny based on our simulations. In

SUBMITTER: Barido-Sottani J 

PROVIDER: S-EPMC6170769 | biostudies-literature | 2018 Sep

REPOSITORIES: biostudies-literature