Simultaneous inference of phylogenetic and transmission trees in infectious disease outbreaks.

ABSTRACT: Whole-genome sequencing of pathogens from host samples becomes more and more routine during infectious disease outbreaks. These data provide information on possible transmission events which can be used for further epidemiologic analyses, such as identification of risk factors for infectivity and transmission. However, the relationship between transmission events and sequence data is obscured by uncertainty arising from four largely unobserved processes: transmission, case observation, within-host pathogen dynamics and mutation. To properly resolve transmission events, these processes need to be taken into account. Recent years have seen much progress in theory and method development, but existing applications make simplifying assumptions that often break up the dependency between the four

SUBMITTER: Klinkenberg D 

PROVIDER: S-EPMC5436636 | biostudies-literature | 2017 May

REPOSITORIES: biostudies-literature