Inferring within‐flock transmission dynamics of highly pathogenic avian influenza H5N8 virus in France, 2020

• Published in: Transboundary and Emerging Diseases
• Main Authors: Vergne, Timothée, Gubbins, Simon, Guinat, Claire, Bauzile, Billy, Delpont, Mattias, Chakraborty, Debapriyo, Gruson, Hugo, Roche, Benjamin, Andraud, Mathieu, Paul, Mathilde, Guérin, Jean-Luc
• Other Authors: Interactions hôtes-agents pathogènes Toulouse (IHAP), Ecole Nationale Vétérinaire de Toulouse (ENVT), Institut National Polytechnique (Toulouse) (Toulouse INP), Université de Toulouse (UT)-Université de Toulouse (UT)-Institut National Polytechnique (Toulouse) (Toulouse INP), Université de Toulouse (UT)-Université de Toulouse (UT)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), The Pirbright Institute, Biotechnology and Biological Sciences Research Council (BBSRC), Department of Biosystems Science and Engineering ETH Zürich (D-BSSE), Eidgenössische Technische Hochschule - Swiss Federal Institute of Technology Zürich (ETH Zürich), Swiss Institute of Bioinformatics Lausanne (SIB), Université de Lausanne = University of Lausanne (UNIL), Maladies infectieuses et vecteurs : écologie, génétique, évolution et contrôle (MIVEGEC), Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD France-Sud ), Sorbonne Université (SU), Universidad Nacional Autónoma de México = National Autonomous University of Mexico (UNAM), Facultad de Medicina Veterinaria y Zootecnia, Laboratoire de Ploufragan-Plouzané-Niort ANSES, Agence nationale de sécurité sanitaire de l'alimentation, de l'environnement et du travail (ANSES), The authors would like to thank the French Ministry of Agriculture and the veterinary services of the Landes department for their support inimplementing this study. The work was carried out within the frame work of the 'Chaire de Biosécurité aviaire' at the 'École Nationale Vétérinaire de Toulouse', which is funded by the French Ministry of Agriculture. CG has received funding from the European Union’s Horizon 2020 research and innovation programme under the Marie Sklodowska-Curie grant agreement No. 842621.SG was funded by the Biotechnology and Biological Sciences Research Council (grant codes: BB/E/I/00007036andBB/E/I/00007037)., European Project: 0842621(2009)
• Format: Article in Journal/Newspaper
• Language: English
• Published: HAL CCSD 2021
• Subjects: avian flu; beta; duck; inference; mechanistic model; mortality; R0; spread; [SDV]Life Sciences [q-bio]; Avian flu
• Online Access: https://hal.inrae.fr/hal-03479732; https://hal.inrae.fr/hal-03479732/document; https://hal.inrae.fr/hal-03479732/file/TED-07-2021.pdf; https://doi.org/10.1111/tbed.14202

International audience Following the emergence of highly pathogenic avian influenza (H5N8) in France in early December 2020, we used duck mortality data from the index farm to investigate within-flock transmission dynamics. A stochastic epidemic model was fitted to the daily mortality data and model parameters were estimated using an approximate Bayesian computation sequential Monte Carlo (ABC-SMC) algorithm. The model predicted that the first bird in the flock was infected 5 days (95% credible interval, CI: 3-6) prior to the day of suspicion and that the transmission rate was 4.1 new infections per day (95% CI: 2.8-5.8). On average, ducks became infectious 4.1 h (95% CI: 0.7-9.1) after infection and remained infectious for 4.3 days (95% CI: 2.8-5.7). The model also predicted that 34% (50% prediction interval: 8%-76%) of birds would already be infectious by the day of suspicion, emphasizing the substantial latent threat this virus could pose to other poultry farms and to neighbouring wild birds. This study illustrates how mechanistic models can help provide rapid relevant insights that contribute to the management of infectious disease outbreaks of farmed animals. These methods can be applied to future outbreaks and the resulting parameter estimates made available to veterinary services within a few hours.