Center for Ecology of Infectious Diseases, Department of Infectious Diseases, Department of Ecology and Biostatistics, Institute of Bioinformatics, University of Georgia, Athens, Georgia, United States of America.
Department of Pathobiology and Veterinary Science, the University of Connecticut, Storrs, Connecticut, United States of America.
PLoS Pathog. 2020 Jan 21;16(1):e1007857. doi: 10.1371/journal.ppat.1007857. eCollection 2020 Jan.
The 2014-2015 highly pathogenic avian influenza (HPAI) H5NX outbreak represents the largest and most expensive HPAI outbreak in the United States to date. Despite extensive traditional and molecular epidemiological studies, factors associated with the spread of HPAI among midwestern poultry premises remain unclear. To better understand the dynamics of this outbreak, 182 full genome HPAI H5N2 sequences isolated from commercial layer chicken and turkey production premises were analyzed using evolutionary models able to accommodate epidemiological and geographic information. Epidemiological compartmental models embedded in a phylogenetic framework provided evidence that poultry type acted as a barrier to the transmission of virus among midwestern poultry farms. Furthermore, after initial introduction, the propagation of HPAI cases was self-sustainable within the commercial poultry industries. Discrete trait diffusion models indicated that within state viral transitions occurred more frequently than inter-state transitions. Distance and sample size were very strongly supported as associated with viral transition between county groups (Bayes Factor > 30.0). Together these findings indicate that the different types of midwestern poultry industries were not a single homogenous population, but rather, the outbreak was shaped by poultry industries and geographic factors.
2014-2015 年高致病性禽流感（HPAI）H5NX 疫情是美国迄今为止规模最大、耗资最多的 HPAI 疫情。尽管进行了广泛的传统和分子流行病学研究，但与中西部家禽养殖场 HPAI 传播相关的因素仍不清楚。为了更好地了解此次疫情的动态，对从商业蛋鸡和火鸡生产场分离的 182 株 HPAI H5N2 全基因组序列进行了分析，使用了能够容纳流行病学和地理信息的进化模型。在进化框架中嵌入的流行病学隔室模型提供了证据，表明家禽类型是中西部家禽养殖场之间病毒传播的障碍。此外，在最初引入后，商业家禽业内部 HPAI 病例的传播具有自我可持续性。离散特征扩散模型表明，州内病毒的转移比州际转移更为频繁。距离和样本量与县组之间的病毒转移密切相关（贝叶斯因子>30.0）。这些发现表明，中西部不同类型的家禽产业不是一个单一的同质群体，而是由家禽产业和地理因素塑造的疫情。
