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Resolving outbreak dynamics using Approximate Bayesian Computation for stochastic birth-death models

By Jarno Lintusaari, Paul Blomstedt, Tuomas Sivula, Michael U. Gutmann, Samuel Kaski, Jukka Corander

Posted 07 Nov 2017
bioRxiv DOI: 10.1101/215533 (published DOI: 10.12688/wellcomeopenres.15048.1)

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. Here we show that the 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 casestudy, we consider the situation where the genotype data are generated as a mixture of three stochastic processes, each with their distinct dynamics and clear epidemiological interpretation. The ABC inference yields stable and accurate posterior inferences about outbreak dynamics from aggregated annual case data with genotype information. We also show that under the proposed model, the infectious population size can be reliably inferred from the data. The estimate is approximately two orders of magnitude smaller compared to assumptions made in the earlier ABC studies, and is much better aligned with epidemiological knowledge about active TB prevalence. Similarly, the reproductive number R related to the primary underlying transmission process is estimated to be nearly three-fold compared with the previous estimates, which has a substantial impact on the interpretation of the fitted outbreak model.

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