Effective control of avian diseases in domestic populations requires understanding of the transmission dynamics facilitating viral emergence and spread. In 2016–17, Italy experienced a significant avian influenza epidemic caused by a highly patho-genic A(H5N8) virus, which affected domestic premises housing around 2.7 mil-lion birds, primarily in the north-eastern regions with the highest density of poultry farms (Lombardy, Emilia-Romagna and Veneto). We perform integrated analyses of genetic, spatiotemporal and host data within a Bayesian phylogenetic framework. Using continuous and discrete phylogeography, we estimate the locations of move-ments responsible for the spread and persistence of the epidemic. The information derived from these analyses on rates of transmission between regions through time can be used to assess the success of control measures. Using an approach based on phylogenetic–temporal distances between domestic cases, we infer the presence of cryptic wild bird-mediated transmission, information that can be used to complement existing epidemiological methods for distinguishing transmission within the domestic population from incursions across the wildlife–domestic interface, a common chal-lenge in veterinary epidemiology. Spatiotemporal reconstruction of the epidemic reveals a highly skewed distribution of virus movements with a high proportion of shorter distance local movements interspersed with occasional long-distance disper-sal events associated with wild birds. We also show how such inference be used to identify possible instances of human-mediated movements where distances be-tween phylogenetically linked domestic cases are unusually high.
Spatiotemporal reconstruction and transmission dynamics during the 2016–17 H5N8 highly pathogenic avian influenza epidemic in Italy