Our understanding of the diversity and evolution of vertebrate RNA viruses is largely limited to those found in mammalian and avian hosts and associated with overt disease. Here, using a large-scale meta-transcriptomic approach, we discover 214 vertebrate-associated viruses in reptiles, amphibians, lungfish, ray-finned fish, cartilaginous fish and jawless fish. The newly discovered viruses appear in every family or genus of RNA virus associated with vertebrate infection, including those containing human pathogens such as influenza virus, the Arenaviridae and Filoviridae families, and have branching orders that broadly reflected the phylogenetic history of their hosts. We establish a long evolutionary history for most groups of vertebrate RNA virus, and support this by evaluating evolutionary timescales using dated orthologous endogenous virus elements. We also identify new vertebrate-specific RNA viruses and genome architectures, and re-evaluate the evolution of vector-borne RNA viruses. In summary, this study reveals diverse virus–host associations across the entire evolutionary history of the vertebrates.Around 200 new vertebrate-specific viruses are discovered, and every vertebrate-specific viral family known to infect mammals and birds is also present in amphibians, reptiles or fish, suggesting that evolution of vertebrate viruses mirrors that of vertebrate hosts.

中文翻译：

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脊椎动物RNA病毒的进化史

我们对脊椎动物 RNA 病毒的多样性和进化的理解主要限于在哺乳动物和鸟类宿主中发现并与明显疾病相关的病毒。在这里，我们使用大规模元转录组学方法，在爬行动物、两栖动物、肺鱼、鳍鱼、软骨鱼和无颚鱼中发现了 214 种脊椎动物相关病毒。新发现的病毒出现在与脊椎动物感染相关的每个 RNA 病毒家族或属中，包括那些含有人类病原体的病毒，如流感病毒、沙粒病毒科和丝状病毒科，并且具有广泛反映宿主系统发育历史的分支顺序。我们为大多数脊椎动物 RNA 病毒群体建立了悠久的进化历史，并通过使用过时的直系同源内源病毒元件评估进化时间尺度来支持这一点。我们还确定了新的脊椎动物特异性 RNA 病毒和基因组结构，并重新评估了载体携带的 RNA 病毒的进化。总之，这项研究揭示了脊椎动物整个进化史中不同的病毒-宿主关联。 发现了大约 200 种新的脊椎动物特异性病毒，并且已知感染哺乳动物和鸟类的每个脊椎动物特异性病毒家族也存在于两栖动物、爬行动物或鱼，表明脊椎动物病毒的进化反映了脊椎动物宿主的进化。