Inferring epidemiologic dynamics from viral evolution: 2014–2015 Eurasian/North American 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 line...

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、野生鸟类及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，而野生鸟类极有可能是2014年欧亚（Eurasian, EA）谱系高致病性禽流感病毒传入北美的源头。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发生了多次重配事件，重配得到的EA/NA H5N2毒株随后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说：（i）野生鸟类体内的新型高致病性禽流感病毒传播受到与高致病性表型相关的机制限制；（ii）此次高致病性禽流感病毒家禽暴发疫情并非自我维持性疫情，而是需要野生鸟类持续提供病毒输入；（iii）欧亚H5N8毒株的重配可产生EA/NA AIV重配毒株，其相较于纯欧亚谱系毒株具备适合度优势...