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bioRxiv · 10.1101/2020.12.21.423436

Inferring within-flock transmission dynamics of highly pathogenic avian influenza (H5N8) in France, 2020

Vergne, T.·Gubbins, S.·Guinat, C.·Bauzile, B.·Delpont, M.·Chakraborty, D.·Gruson, H.·Roche, B.·Andraud, M.·Paul, M.·Guerin, J.-L.
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Abstract

Following the emergence of highly pathogenic avian influenza (H5N8) in France in early December 2020, we used duck mortality data of the index case to investigate within-flock transmission dynamics. A stochastic epidemic model was adjusted to the daily mortality data and model parameters were estimated using an approximate Bayesian computation sequential Monte Carlo (ABC-SMC) algorithm. Results suggested that the virus was introduced 4 days (95% credible interval: 3 - 5) prior to the day suspicion was reported and that the transmission rate was 3.7 day-1 (95%CI: 2.6 - 5.3). On average, ducks started being infectious 3.1 hours (95%CI: 0.4 - 8.0) after infection and remained infectious for 4.4 days (95%CI: 3.1 - 5.6). Model outputs also suggested that the number of infectious ducks was already 3239 (95%CI: 26 - 3706) the day before suspicion, emphasising the substantial latent threat this virus could pose to other poultry farms and to neighbouring wildlife. These estimations can be applied to upcoming outbreaks and made available to veterinary services within few hours. This study illustrates how mechanistic models can provide rapid relevant insights to contribute to the management of infectious disease outbreaks of farmed animals.

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Vergne, T., Gubbins, S., Guinat, C., Bauzile, B., Delpont, M., Chakraborty, D., Gruson, H., Roche, B., Andraud, M., Paul, M., Guerin, J.-L.. 2020-12-21. Inferring within-flock transmission dynamics of highly pathogenic avian influenza (H5N8) in France, 2020. https://doi.org/10.1101/2020.12.21.423436

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