To better understand the origin and evolutionary history of vertebrate viruses, Shi et al. performed a large-scale meta-transcriptomics survey of potential RNA viruses in 186 vertebrate species that represent the vast diversity of the phylum Chordata, including mammals, reptiles, birds, amphibians and different classes of fish. The authors extracted total RNA from the gut, liver and lung or gill from these animals and performed high-throughput RNA sequencing. In their analysis of the sequences, they screened for RNA viruses and identified 214 new putative viral species of which 196 can be considered vertebrate-specific. The authors observed that every vertebrate-specific viral family or genus that is known to infect mammals and birds is also present in reptiles, amphibians or fish, and, moreover, they found a number of viruses that belong to families that had not been previously found in fish or amphibians. For example, they identified influenza viruses in jawless fish, amphibians and ray-finned fish, the latter of which was found to form a sister-group to human influenza B virus. They also found that the newly described viruses shared tissue tropism with their mammalian counterpart; members of the genus Hepacivirus were found in the liver, whereas members of the Picornaviridae, Calciviridae and Astroviridae families were found in the gut.
The authors constructed phylogenetic trees that revealed the evolutionary relationships between the newly identified viruses and found that the phylogenetic history of the RNA viruses mirror that of their hosts over long evolutionary timescales, which implies that RNA viruses followed a similar evolutionary trajectory as their vertebrate hosts, co-evolving with them for millions of years. Their proposed evolutionary trajectories for RNA viruses were calibrated and supported by comparisons using dated orthologous endogenous retroviruses. Although they found that each vertebrate class is dominated by a specific set of RNA viruses, some of the viruses were found to infect multiple hosts, which indicates that in addition to co-divergence, cross species transmissions had regularly occurred and were sustained throughout evolutionary history.
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