Quantifying Transmission Heterogeneity Using Both Pathogen Phylogenies and Incidence Time Series.

ABSTRACT: Heterogeneity in individual-level transmissibility can be quantified by the dispersion parameter k of the offspring distribution. Quantifying heterogeneity is important as it affects other parameter estimates, it modulates the degree of unpredictability of an epidemic, and it needs to be accounted for in models of infection control. Aggregated data such as incidence time series are often not sufficiently informative to estimate k. Incorporating phylogenetic analysis can help to estimate k concurrently with other epidemiological parameters. We have developed an inference framework that uses particle Markov Chain Monte Carlo to estimate k and other epidemiological parameters using both incidence time series and the pathogen phylogeny. Using the framework to fit a modified compartmental trans

SUBMITTER: Li LM 

PROVIDER: S-EPMC5850343 | biostudies-literature | 2017 Nov

REPOSITORIES: biostudies-literature