Data from: Inferring epidemiologic dynamics from viral evolution: 2014-2015 EA/NA highly pathogenic avian influenza viruses exceed transmission threshold, R0=1, in wild birds and poultry in North America

Highly pathogenic avian influenza virus (HPAIV) is a multi-host pathogen with lineages that pose health risks for domestic birds, wild birds, and humans. One mechanism of intercontinental HPAIV spread is through wild bird reservoirs and wild birds were the likely sources of a Eurasian (EA) lineage HPAIV into North America in 2014. The introduction resulted in several reassortment events with North American (NA) lineage low pathogenic avian influenza viruses and the reassortant EA/NA H5N2 went on to cause one of the largest HPAIV poultry outbreaks in North America. We evaluated three hypotheses about novel HPAIV introduced into wild and domestic bird hosts: (i) transmission of novel HPAIVs in wild birds was restricted by mechanisms associated with highly-pathogenic phenotypes; (ii) the HPAIV poultry outbreak was not self-sustaining and required viral input from wild birds; (iii) reassortment of the EA H5N8 generated reassortant EA/NA AIVs with a fitness advantage over fully Eurasian lineages in North American wild birds. We used a time-rooted phylodynamic model that explicitly incorporated viral population dynamics with evolutionary dynamics to estimate the basic reproductive number (R0) and viral migration among host types in domestic and wild birds, as well as between the EA H5N8 and EA/NA H5N2 in wild birds. We did not find evidence to support hypothesis (i) or (ii) as our estimates of the transmission parameters suggested that the HPAIV outbreak met or exceeded the threshold for persistence in wild birds (R0 > 1) and poultry (R0 ≈ 1) with minimal estimated transmission among host types. There was also no evidence to support hypothesis (iii) because R0 values were similar among EA H5N8 and EA/NA H5N2 in wild birds. Our results suggest that this novel HPAIV and reassortments did not encounter any transmission barriers sufficient to prevent persistence when introduced to wild or domestic birds.

高致病性禽流感病毒（Highly pathogenic avian influenza virus, HPAIV）是一种多宿主病原体，其不同谱系对家禽、野生鸟类与人类均构成健康风险。跨洲际高致病性禽流感病毒传播的途径之一是借助野生鸟类宿主库，2014年欧亚（Eurasian, EA）谱系的高致病性禽流感病毒传入北美，其潜在源头即为野生鸟类。此次病毒引入事件与北美（North American, NA）谱系的低致病性禽流感病毒（low pathogenic avian influenza viruses）发生了多次重配事件，最终重配产生的EA/NA H5N2毒株引发了北美地区规模最大的高致病性禽流感家禽暴发疫情之一。本研究针对引入野生与家禽宿主的新型高致病性禽流感病毒提出了三项假设：（i）野生鸟类中的新型高致病性禽流感病毒传播受到与高致病表型相关的机制限制；（ii）此次高致病性禽流感家禽暴发并非自我维持，而是需要野生鸟类持续提供病毒输入；（iii）欧亚H5N8毒株的重配产生了EA/NA禽流感病毒，该重配毒株在北美野生鸟类中相比完全欧亚谱系毒株具有适合度优势。本研究采用时间根系统发育动力学模型（time-rooted phylodynamic model），该模型将病毒种群动态与进化动态明确结合，用于估算基本再生数（basic reproductive number, R₀）以及宿主类型间（家禽与野生鸟类之间）、野生鸟类中欧亚H5N8与EA/NA H5N2毒株间的病毒迁移情况。研究未发现支持假设（i）或（ii）的证据：我们的传播参数估算结果显示，该高致病性禽流感疫情在野生鸟类中的基本再生数满足或超过持续传播阈值（R₀>1），在家禽中基本再生数约为1（R₀≈1），且宿主类型间的传播水平极低。同时也没有证据支持假设（iii），因为野生鸟类中欧亚H5N8与EA/NA H5N2毒株的基本再生数数值相近。本研究结果表明，这类新型高致病性禽流感病毒及其重配毒株在引入野生或家禽宿主后，未遭遇足以阻断其持续传播的传播障碍。