Inferring Viral Transmission Time from Phylogenies for Known Transmission Pairs.

ABSTRACT: When the time of an HIV transmission event is unknown, methods to identify it from virus genetic data can reveal the circumstances that enable transmission. We developed a single-parameter Markov model to infer transmission time from an HIV phylogeny constructed of multiple virus sequences from people in a transmission pair. Our method finds the statistical support for transmission occurring in different possible time slices. We compared our time-slice model results to previously described methods: a tree-based logical transmission interval, a simple parsimony-like rules-based method, and a more complex coalescent model. Across simulations with multiple transmitted lineages, different transmission times relative to the source's infection, and different sampling times relative to transmissi

SUBMITTER: Goldberg EE 

PROVIDER: S-EPMC10776241 | biostudies-literature | 2024 Jan

REPOSITORIES: biostudies-literature