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亚型疫情在过去十年间于美洲地区暴发三次，给受影响区域造成了严重的经济损失。2012年6月/7月，墨西哥哈利斯科州的商业养殖场首次暴发新型高致病性H7N3禽流感疫情，直至2013年8月，墨西哥境内邻近各州仍陆续检出该疫情。为探究本次疫情的起源，研究团队基于北美地区全长禽流感病毒的8个基因组片段序列，使用BEAST软件构建了时间分辨系统发育树。研究以连续时间马尔可夫链为模型，将病毒的地理位置、亚型、禽类宿主种类及致病性设为离散性状，纳入系统发育树分析。随后，研究团队采用分层系统发育模型（HPM）对各基因组片段开展联合分析，实现了不同片段间地理位置、亚型、宿主种类等性状演化速率的联合推断。研究借助虚拟地球软件完整可视化了病毒的空间扩散全过程。分析结果表明，本次墨西哥暴发的高致病性H7N3禽流感病毒源自北美地区庞大的低致病性禽流感病毒种群，经复杂的基因重配事件演化而来。该病毒的不同基因组片段分别来自北美不同迁徙路线上的野生水禽：8个基因组片段中的5个（血凝素（HA）、神经氨酸酶（NA）、核蛋白（NP）、基质蛋白（M）、非结构蛋白（NS））源自沿北美中部迁徙路线迁徙的野生鸟类，剩余的聚合酶碱性蛋白2（PB2）、聚合酶碱性蛋白1（PB1）与聚合酶酸性蛋白（PA）三个片段，则来自沿北美西部迁徙路线迁徙的野生鸟类。上述研究结果提示，墨西哥或为病毒基因重配的热点区域——由于来自不同迁徙路线的野生鸟类会在冬季在此集结，为病毒基因重配提供了理想的交汇场所。