PHYLOSCANNER: Inferring Transmission from Within- and Between-Host Pathogen Genetic Diversity.

ABSTRACT: A central feature of pathogen genomics is that different infectious particles (virions and bacterial cells) within an infected individual may be genetically distinct, with patterns of relatedness among infectious particles being the result of both within-host evolution and transmission from one host to the next. Here, we present a new software tool, phyloscanner, which analyses pathogen diversity from multiple infected hosts. phyloscanner provides unprecedented resolution into the transmission process, allowing inference of the direction of transmission from sequence data alone. Multiply infected individuals are also identified, as they harbor subpopulations of infectious particles that are not connected by within-host evolution, except where recombinant types emerge. Low-level contaminati

SUBMITTER: Wymant C 

PROVIDER: S-EPMC5850600 | biostudies-literature | 2018 Mar

REPOSITORIES: biostudies-literature