Bayesian reconstruction of transmission within outbreaks using genomic variants.

ABSTRACT: Pathogen genome sequencing can reveal details of transmission histories and is a powerful tool in the fight against infectious disease. In particular, within-host pathogen genomic variants identified through heterozygous nucleotide base calls are a potential source of information to identify linked cases and infer direction and time of transmission. However, using such data effectively to model disease transmission presents a number of challenges, including differentiating genuine variants from those observed due to sequencing error, as well as the specification of a realistic model for within-host pathogen population dynamics. Here we propose a new Bayesian approach to transmission inference, BadTrIP (BAyesian epiDemiological TRansmission Inference from Polymorphisms), that explicitly mod

SUBMITTER: De Maio N 

PROVIDER: S-EPMC5927459 | biostudies-literature | 2018 Apr

REPOSITORIES: biostudies-literature