Integration of viruses into host genomes can give rise to endogenous viral elements (EVEs), which provide insights into viral diversity, host range and evolution. A systematic search for EVEs is becoming computationally challenging given the available genomic data. We used a cloud-computing approach to perform a comprehensive search for EVEs in the kingdoms Shotokuvirae and Orthornavirae across vertebrates. We identified 2,040 EVEs in 295 vertebrate genomes and provide evidence for EVEs belonging to the families Chuviridae, Paramyxoviridae, Nairoviridae and Benyviridae. We also find an EVE from the Hepacivirus genus of flaviviruses with orthology across murine rodents. In addition, our analyses revealed that reptarenaviruses and filoviruses probably acquired their glycoprotein ectodomains three times independently from retroviral elements. Taken together, these findings encourage the addition of 4 virus families and the Hepacivirus genus to the growing virus fossil record of vertebrates, providing key insights into their natural history and evolution.

将病毒整合到宿主基因组中可产生内源性病毒元件 （EVE），从而深入了解病毒多样性、宿主范围和进化。鉴于可用的基因组数据，对 EVE 的系统搜索在计算上变得具有挑战性。我们使用云计算方法在脊椎动物的 Shotokuvirae 和 Orthornavirae 界中对 EVE 进行了全面搜索。我们在 2,040 个脊椎动物基因组中鉴定了 295 个 EVE，并为属于 Chuviridae、Paramyxoviridae、Nairoviridae 和 Benyviridae 的 EVE 提供了证据。我们还发现了来自黄病毒Hepacivirus属的EVE在小鼠啮齿动物中具有正交。此外，我们的分析表明，repthanavirus 和 filoviruses 可能独立于逆转录病毒元件获得其糖蛋白胞外结构域 3 次。综上所述，这些发现鼓励将 4 个病毒科和肝病毒属添加到不断增长的脊椎动物病毒化石记录中，从而为了解它们的自然历史和进化提供关键见解。