tetano
Editor, Senior Moderator
Transbound Emerg Dis
. 2022 Feb 23.
doi: 10.1111/tbed.14490. Online ahead of print.
Phylodynamic analysis of the highly pathogenic avian influenza H5N8 epidemic in France, 2016-17
Debapriyo Chakraborty[SUP] 1 [/SUP], Claire Guinat[SUP] 2 3 [/SUP], Nicola F Müller[SUP] 4 [/SUP], Francois-Xavier Briand[SUP] 5 [/SUP], Mathieu Andraud[SUP] 5 [/SUP], Axelle Scoizec[SUP] 5 [/SUP], Sophie Lebouquin[SUP] 5 [/SUP], Eric Niqueux[SUP] 5 [/SUP], Audrey Schmitz[SUP] 5 [/SUP], Beatrice Grasland[SUP] 5 [/SUP], Jean-Luc Guerin[SUP] 1 [/SUP], Mathilde C Paul[SUP] 1 [/SUP], Timothée Vergne[SUP] 1 [/SUP]
Affiliations
Abstract
In 2016-17, France experienced a devastating epidemic of highly pathogenic avian influenza (HPAI) H5N8, with more than 400 outbreaks reported in poultry farms. We analysed the spatio-temporal 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 generalised 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 characterising the dynamics of a HPAI epidemic and assessing control measures. This method can be adapted to investigate other epidemics of fast-evolving livestock pathogens. This article is protected by copyright. All rights reserved.
Keywords: Emerging infectious diseases; Modelling infectious disease dynamics; Outbreak analytics; Reconstruction of viral transmission; Virus evolution; Virus molecular epidemiology.
. 2022 Feb 23.
doi: 10.1111/tbed.14490. Online ahead of print.
Phylodynamic analysis of the highly pathogenic avian influenza H5N8 epidemic in France, 2016-17
Debapriyo Chakraborty[SUP] 1 [/SUP], Claire Guinat[SUP] 2 3 [/SUP], Nicola F Müller[SUP] 4 [/SUP], Francois-Xavier Briand[SUP] 5 [/SUP], Mathieu Andraud[SUP] 5 [/SUP], Axelle Scoizec[SUP] 5 [/SUP], Sophie Lebouquin[SUP] 5 [/SUP], Eric Niqueux[SUP] 5 [/SUP], Audrey Schmitz[SUP] 5 [/SUP], Beatrice Grasland[SUP] 5 [/SUP], Jean-Luc Guerin[SUP] 1 [/SUP], Mathilde C Paul[SUP] 1 [/SUP], Timothée Vergne[SUP] 1 [/SUP]
Affiliations
- PMID: 35195353
- DOI: 10.1111/tbed.14490
Abstract
In 2016-17, France experienced a devastating epidemic of highly pathogenic avian influenza (HPAI) H5N8, with more than 400 outbreaks reported in poultry farms. We analysed the spatio-temporal 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 generalised 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 characterising the dynamics of a HPAI epidemic and assessing control measures. This method can be adapted to investigate other epidemics of fast-evolving livestock pathogens. This article is protected by copyright. All rights reserved.
Keywords: Emerging infectious diseases; Modelling infectious disease dynamics; Outbreak analytics; Reconstruction of viral transmission; Virus evolution; Virus molecular epidemiology.