Data from: A synchronized global sweep of the internal genes of modern avian influenza virus

Zoonotic infectious diseases such as influenza continue to pose a grave threat to human health. However, the factors that mediate the emergence of RNA viruses such as influenza A virus (IAV) are still incompletely understood. Phylogenetic inference is crucial to reconstructing the origins and tracing the flow of IAV within and between hosts. Here we show that explicitly allowing IAV host lineages to have independent rates of molecular evolution is necessary for reliable phylogenetic inference of IAV and that methods that do not do so, including ‘relaxed’ molecular clock models, can be positively misleading. A phylogenomic analysis using a host-specific local clock model recovers extremely consistent evolutionary histories across all genomic segments and demonstrates that the equine H7N7 lineage is a sister clade to strains from birds—as well as those from humans, swine and the equine H3N8 lineage—sharing an ancestor with them in the mid to late 1800s. Moreover, major western and eastern hemisphere avian influenza lineages inferred for each gene coalesce in the late 1800s. On the basis of these phylogenies and the synchrony of these key nodes, we infer that the internal genes of avian influenza virus (AIV) underwent a global selective sweep beginning in the late 1800s, a process that continued throughout the twentieth century and up to the present. The resulting western hemispheric AIV lineage subsequently contributed most of the genomic segments to the 1918 pandemic virus and, independently, the 1963 equine H3N8 panzootic lineage. This approach provides a clear resolution of evolutionary patterns and processes in IAV, including the flow of viral genes and genomes within and between host lineages.流感等人畜共患传染病始终对人类健康构成严重威胁。然而，甲型流感病毒（influenza A virus, IAV）这类RNA病毒的出现机制仍未完全阐明。系统发育推断（phylogenetic inference）对于重构IAV的起源以及追溯其在宿主内和宿主间的传播路径至关重要。本研究表明，若要对IAV进行可靠的系统发育推断，必须明确允许IAV宿主谱系拥有独立的分子进化速率；而未采用该策略的方法（包括宽松分子钟（relaxed molecular clock）模型）甚至会产生误导性结果。本研究采用宿主特异性局部分子钟模型开展系统基因组分析（phylogenomic analysis），成功解析出所有基因组片段的进化历史均呈现高度一致性，且马源H7N7谱系与鸟类、人类、猪以及马源H3N8谱系的毒株构成姊妹支系，三者的共同祖先可追溯至19世纪中后期。此外，通过各基因推断得到的主要东、西半球禽流感谱系均在19世纪后期发生溯祖事件。基于上述系统发育结果以及这些关键节点的同步性，本研究推断禽流感病毒（avian influenza virus, AIV）的内部基因于19世纪后期开始经历全球性选择性清除事件，该过程贯穿整个20世纪并延续至今。由此产生的西半球AIV谱系随后为1918年大流行毒株提供了绝大多数基因组片段，同时也独立贡献了1963年马源H3N8兽疫大流行谱系的基因组片段。本研究采用的分析方法可清晰阐明IAV的进化模式与进化过程，包括病毒基因及基因组在宿主谱系内部以及宿主谱系间的传播流动。