Phylodynamic assessment of control measures of a highly pathogenic avian influenza outbreak in France
Debapriyo Chakraborty *, Claire Guinat2,3, Nicola F. Müller4, Francois-Xavier Briand5, Mathieu Andraud5, Axelle Scoizec5, Sophie Lebouquin5, Eric Niqueux5, Audrey Schmitz5, Beatrice Grasland5, Jean-Luc Guerin1, Mathilde C. Paul1 and Timothée Vergne1
1INRAE ENVT Mixed Research Unit on Host-Pathogenic Agents Interactions (IHAP), National Veterinary School of Toulouse (ENVT), Toulouse, France 2Department of Biosystems Science and Engineering, ETH Zurich, Basel, Switzerland 3Swiss Institute of Bioinformatics (SIB), Switzerland 4Vaccine and Infectious Disease, Fred Hutchinson Cancer Research Centre, Seattle, Washington State, USA 5The French Agency for Food, Environmental and Occupational Health & Safety (ANSES) Laboratory of Ploufragan-Plouzané-Niort, Ploufragan, France
*Corresponding author email: debapriyoc@gmail.com
Phylodynamic methods have successfully been used to describe viral spread history but their application in assessing specific control measures are rare. In 2016-17, France experienced a devastating epidemic of a highly pathogenic avian influenza A virus (H5N8; clade 2.3.4.4b). Using 196 viral genomes, we conducted a phylodynamic analysis combined with generalised linear model and showed that the large-scale preventive culling of ducks significantly reduced the viral spread between départements (French administrative division). We also found that the virus likely spread more frequently between départements that shared borders, but the spread was not found to be linked to duck transport between départements. Duck transport within départements increased the within-département transmission intensity, although the association was weak. 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, by testing specific hypothesis related to different control measures, we demonstrated the capability of phylodynamics methods in investigating the impact of control measures on viral epidemiology.