Methods Combining Genomic and Epidemiological Data in the Reconstruction of Transmission Trees: A Systematic Review.

ABSTRACT: In order to better understand transmission dynamics and appropriately target control and preventive measures, studies have aimed to identify who-infected-whom in actual outbreaks. Numerous reconstruction methods exist, each with their own assumptions, types of data, and inference strategy. Thus, selecting a method can be difficult. Following PRISMA guidelines, we systematically reviewed the literature for methods combing epidemiological and genomic data in transmission tree reconstruction. We identified 22 methods from the 41 selected articles. We defined three families according to how genomic data was handled: a non-phylogenetic family, a sequential phylogenetic family, and a simultaneous phylogenetic family. We discussed methods according to the data needed as well as the underlying seq

SUBMITTER: Duault H 

PROVIDER: S-EPMC8875843 | biostudies-literature | 2022 Feb

REPOSITORIES: biostudies-literature