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bioRxiv · 10.1101/2025.11.11.687876

Parameterisation of epidemiological models from small field experiments: a case study of banana bunchy top virus transmission

Retkute, R.·Omondi, A. B.·Soko, M.·Staver, C.·Thomas, J. E.·Gilligan, C. A.
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Abstract

Accurate estimation of epidemiological parameters from limited field data remains a major challenge in plant disease modeling. We present a novel data-augmented adaptive multiple importance sampling (DA-AMIS) framework that integrates Bayesian inference with stochastic epidemic modeling to estimate key transmission parameters from small field experiments. Using detailed individual-level observations from a 24-plant experiment on the natural spread of banana bunchy top virus (BBTV) in Benin, we jointly inferred infection timing, dispersal characteristics, and transmission rates for both primary and secondary infections. Model validation against independent datasets from BBTV field trials in Burundi and Malawi showed close correspondence between simulated and observed prevalence dynamics, confirming the generality of parameter estimates across regions. The inferred 12% infection rate of replanting suckers underscores the risk of disease introduction through planting material, while simulations identified April as the period of peak infection, providing actionable insights for surveillance timing.

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Retkute, R., Omondi, A. B., Soko, M., Staver, C., Thomas, J. E., Gilligan, C. A.. 2025-11-12. Parameterisation of epidemiological models from small field experiments: a case study of banana bunchy top virus transmission. https://doi.org/10.1101/2025.11.11.687876

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