Data from: Determining the phylogenetic and phylogeographic origin of highly pathogenic avian influenza (H7N3) in Mexico

Highly pathogenic (HP) avian influenza virus (AIV) H7N3 outbreaks occurred 3 times in the Americas in the past 10 years and caused severe economic loss in the affected regions. In June/July 2012, new HP H7N3 outbreaks occurred at commercial farms in Jalisco, Mexico. Outbreaks continued to be identified in neighbouring states in Mexico till August 2013. To explore the origin of this outbreak, time resolved phylogenetic trees were generated from the eight segments of full-length AIV sequences in North America using BEAST. Location, subtype, avian host species and pathogenicity were modelled as discrete traits upon the trees using continuous time Markov chains. A further joint analysis among segments was performed using a hierarchical phylogenetic model (HPM) which allowed trait rates (location, subtype, host species) to be jointly inferred across different segments. The complete spatial diffusion process was visualised through virtual globe software. Our result indicated the Mexico HP H7N3 originated from the large North America low pathogenicity AIV pool through complicated reassortment events. Different segments were contributed by wild waterfowl from different N. American flyways. Five of the eight segments (HA, NA, NP, M, NS) were introduced from wild birds migrating along the central North American flyway, and PB2, PB1 and PA were introduced via the western North American flyway. These results highlight a potential role for Mexico as a hotspot of virus reassortment as it is where wild birds from different migration routes mix during the winter.

高致病性（HP）禽流感病毒（AIV）H7N3近十年在美洲已暴发三次，给受影响地区造成了严重的经济损失。2012年6/7月，墨西哥哈利斯科州的商业养殖场暴发了新型高致病性H7N3疫情，直至2013年8月，墨西哥周边各州仍陆续检出该疫情。为探究此次疫情的起源，研究团队基于北美地区全长禽流感病毒的8个基因节段序列，使用BEAST软件构建了时间分辨系统发育树。本研究以连续时间马尔可夫链模型，将采样地点、病毒亚型、禽类宿主种类及致病性设为树结构上的离散特征进行建模；同时采用层级系统发育模型（HPM）对各基因节段开展联合分析，实现不同节段间的特征演化速率（采样地点、亚型、宿主种类）的联合推断。借助虚拟地球软件，完整可视化了病毒的空间扩散过程。研究结果显示，此次墨西哥暴发的高致病性H7N3疫情源自北美地区广泛存在的低致病性禽流感病毒库，经历了复杂的重配事件：各基因节段分别来自北美不同迁徙路线的野生水禽，其中8个基因节段中的5个（HA、NA、NP、M、NS）源自沿北美中部迁徙路线迁徙的野生鸟类，而PB2、PB1和PA则经由北美西部迁徙路线传入。本次研究结果凸显了墨西哥作为病毒重配热点区域的潜在可能——该国是不同迁徙路线野生鸟类冬季汇合的场所。