Nature2014-06-19 2:19 PM

禽流感病毒的历史 A synchronized global sweep of the internal genes of modern avian influenza virus

论文摘要 

我们对RNA病毒如“甲流”病毒作为对人类健康的威胁出现背后的因素仍然不是完全了解。在这篇论文中,Michael Worobey等人提出了跟踪禽流感病毒演变的一个新方法。他们的宿主特异性“本地时钟”(local clock)模型将各种不同病毒宿主世系的独立分子演变速度考虑了进去。系统发育基因组分析表明在所有基因组区段存在一个一致的演化史,同时也识别出马的H7N7世系是来自鸟类的毒株的一个姐妹演化枝,也是来自人类、猪和马的H3N8世系的一个姐妹演化枝,在19世纪与它们共享一个祖先。这样所产生的西半球禽流感病毒世系随后为1918年大流行的病毒贡献了其基因组片段的大部分,同时也为1963年的马H3N8兽疫世系独立贡献了基因组片段。

Abstract 

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 models9, 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.

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