Agricultural and geographic factors shaped the North American 2015 highly pathogenic avian influenza H5N2 outbreak

Abstract

16 KEYWORDS: highly pathogenic avian influenza, phylogenetics, phylodynamcs, avian disease, 17 Bayesian inference, coalescent models, discrete trait evolution, generalized linear model 18 2 19 ABSTRACT 20 The 2014 -2015 highly pathogenic avian influenza (HPAI) H5NX outbreak represents the 21 largest and most expensive HPAI outbreak in the United States to date. Despite extensive 22 traditional and molecular epidemiological studies, factors associated with the spread of HPAI 23 among midwestern poultry premises remain unclear. To better understand the dynamics of this 24 outbreak, 182 full genome HPAI H5N2 sequences isolated from commercial layer chicken and 25 turkey production premises were analyzed using evolutionary models modified to incorporate 26 epidemiological and geographic information. Epidemiological compartmental models 27 constructed in a phylogenetic framework provided evidence that poultry type acted as a barrier to 28 the transmission of virus among midwestern poultry farms. Furthermore, after initial 29 introduction, a continuous external source of virus was not needed to explain the propagation of 30 HPAI cases within the commercial poultry industries. Discrete trait diffusion models indicated 31 that within state viral transitions occurred more frequently than inter-state transitions. Distance, 32 road density and proportion of water coverage were all supported as associated with viral 33 transition between county groups (Bayes Factor > 3.0). Together these findings indicate that the 34 midwestern poultry industries were not a single homogenous population, but rather, the outbreak 35 was shaped by poultry sectors and geographic factors.