Deep-mining of vertebrate genomes reveals an unexpected diversity of endogenous viral elements

Endogenous viral elements (EVEs) are key to our understanding of the diversity, host range and evolutionary history of viruses. Given the increasing amounts of virus and host sequence data, a systematic search for EVEs is becoming computationally challenging. We used ElasticBLAST on the Google Cloud Platform to perform a comprehensive search for EVEs (kingdoms Shotokuvirae and Orthornavirae) across vertebrates. We provide evidence for the first EVEs belonging to the families Chuviridae, Paramyxoviridae, Nairoviridae and Benyviridae in vertebrate genomes. We also find an EVE from the Hepacivirus genus of flaviviruses with orthology across murine rodents. Phylogenetic analysis of hits closely related to reptarenavirus and filovirus ectodomains suggest three independent captures from a retroviral source. Our findings increase the family-level diversity of non-retroviral EVEs in vertebrates by 44%. In particular, our results shed light on key aspects of the natural history and evolution of viruses in the phyla Negarnaviricota and Kitrinoviricota.