Phylogenetic tree

Virus

Evolutionary biology

Biology

Phylogenetics

Gene

Genome

Human virome

Vertebrate

RNA virus

Viral evolution

Genetics

Nature

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.

The evolutionary history of vertebrate RNA viruses