Phylodynamic analysis of the highly pathogenic avian influenza H5N8 epidemic in France, 2016-2017.

ABSTRACT: 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 a

SUBMITTER: Chakraborty D 

PROVIDER: S-EPMC9790735 | biostudies-literature | 2022 Sep

REPOSITORIES: biostudies-literature