Phylodynamic analysis of the highly pathogenic avian influenza H5N8 epidemic in France, 2016-2017.
emerging infectious diseases
modelling infectious disease dynamics
outbreak analytics
reconstruction of viral transmission
virus evolution
virus molecular epidemiology
Journal
Transboundary and emerging diseases
ISSN: 1865-1682
Titre abrégé: Transbound Emerg Dis
Pays: Germany
ID NLM: 101319538
Informations de publication
Date de publication:
Sep 2022
Sep 2022
Historique:
revised:
14
01
2022
received:
14
08
2021
accepted:
15
02
2022
pubmed:
24
2
2022
medline:
30
9
2022
entrez:
23
2
2022
Statut:
ppublish
Résumé
In 2016-2017, France experienced a devastating epidemic of highly pathogenic avian influenza (HPAI) H5N8, with more than 400 outbreaks reported in poultry farms. We analyzed the spatiotemporal dynamics of the epidemic using a structured-coalescent-based phylodynamic approach that combined viral genomic data (n = 196; one viral genome per farm) and epidemiological data. In the process, we estimated viral migration rates between départements (French administrative regions) and the temporal dynamics of the effective viral population size (Ne) in each département. Viral migration rates quantify viral spread between départements and Ne is a population genetic measure of the epidemic size and, in turn, is indicative of the within-département transmission intensity. We extended the phylodynamic analysis with a generalized linear model to assess the impact of multiple factors-including large-scale preventive culling and live-duck movement bans-on viral migration rates and Ne. We showed that the large-scale culling of ducks that was initiated on 4 January 2017 significantly reduced the viral spread between départements. No relationship was found between the viral spread and duck movements between départements. The within-département transmission intensity was found to be weakly associated with the intensity of duck movements within départements. Together, these results indicated that the virus spread in short distances, either between adjacent départements or within départements. Results also suggested that the restrictions on duck transport within départements might not have stopped the viral spread completely. Overall, we demonstrated the usefulness of phylodynamics in characterizing the dynamics of a HPAI epidemic and assessing control measures. This method can be adapted to investigate other epidemics of fast-evolving livestock pathogens.
Identifiants
pubmed: 35195353
doi: 10.1111/tbed.14490
pmc: PMC9790735
doi:
Types de publication
Journal Article
Langues
eng
Sous-ensembles de citation
IM
Pagination
e1574-e1583Subventions
Organisme : FEDER/Région Occitanie Recherche et Sociétés 2018-AI-TRACK
Organisme : PREDYT project (Fonds de la Recherche pour l'Influenza Aviaire 2019)
Organisme : the Direction Generale de l'Alimentation, Ministère de l'Agriculture et de l'Alimentation, France
Organisme : the Swiss National Science Foundation
Organisme : the European Union's Horizon 2020
Informations de copyright
© 2022 The Authors. Transboundary and Emerging Diseases published by Wiley-VCH GmbH.
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