Identifying Impacts of Contact Tracing on Epidemiological Inference from Phylogenetic Data.

ABSTRACT: Robust sampling methods are foundational to inferences using phylogenies. Yet the impact of using contact tracing, a type of non-uniform sampling used in public health applications such as infectious disease outbreak investigations, has not been investigated in the molecular epidemiology field. To understand how contact tracing influences a recovered phylogeny, we developed a new simulation tool called SEEPS (Sequence Evolution and Epidemiological Process Simulator) that allows for the simulation of contact tracing and the resulting transmission tree, pathogen phylogeny, and corresponding virus genetic sequences. Importantly, SEEPS takes within-host evolution into account when generating pathogen phylogenies and sequences from transmission histories. Using SEEPS, we demonstrate that contac

SUBMITTER: Kupperman MD 

PROVIDER: S-EPMC10705478 | biostudies-literature | 2024 Sep

REPOSITORIES: biostudies-literature