Department of Biology, University of Oxford, Oxford, UK.
Nat Microbiol. 2024 Nov;9(11):3013-3024. doi: 10.1038/s41564-024-01825-4. Epub 2024 Oct 22.
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.
病毒整合到宿主基因组中会产生内源性病毒元件 (EVEs)，这为病毒多样性、宿主范围和进化提供了线索。鉴于现有基因组数据，对 EVEs 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 王国中全面搜索 EVEs。我们在 295 个脊椎动物基因组中鉴定出 2040 个 EVEs，并提供了属于 Chuviridae、Paramyxoviridae、Nairoviridae 和 Benyviridae 家族的 EVEs 的证据。我们还发现了一个来自黄病毒属的 Hepacivirus 属的 EVE，在鼠科啮齿动物中有同源性。此外，我们的分析表明， reptarenaviruses 和 filoviruses 可能从逆转录病毒元件中独立获得了 3 次糖蛋白外显子。总之，这些发现鼓励将 4 个病毒科和 Hepacivirus 属添加到不断增长的脊椎动物病毒化石记录中，为它们的自然历史和进化提供了关键见解。
