Resolving outbreak dynamics using approximate bayesian computation for stochastic birth-death models

Earlier research has suggested that approximate Bayesian computation (ABC) makes it possible to fit simulator-based intractable birth–death models to investigate communicable disease outbreak dynamics with accuracy comparable to that of exact Bayesian methods. However, recent findings have indicated that key parameters, such as the reproductive number R, may remain poorly identifiable with these models. Here we show that this identifiability issue can be resolved by taking into account disease-specific characteristics of the transmission process in closer detail. Using tuberculosis (TB) in the San Francisco Bay area as a case study, we consider a model that generates genotype data from a mixture of three stochastic processes, each with its own distinct dynamics and clear epidemiological interpretation