Shared Genomic Variants: Identification of Transmission Routes Using Pathogen Deep-Sequence Data.

ABSTRACT: Sequencing pathogen samples during a communicable disease outbreak is becoming an increasingly common procedure in epidemiologic investigations. Identifying who infected whom sheds considerable light on transmission patterns, high-risk settings and subpopulations, and the effectiveness of infection control. Genomic data shed new light on transmission dynamics and can be used to identify clusters of individuals likely to be linked by direct transmission. However, identification of individual routes of infection via single genome samples typically remains uncertain. We investigated the potential of deep sequence data to provide greater resolution on transmission routes, via the identification of shared genomic variants. We assessed several easily implemented methods to identify transmission

SUBMITTER: Worby CJ 

PROVIDER: S-EPMC5860558 | biostudies-literature | 2017 Nov

REPOSITORIES: biostudies-literature