Foamy-like Endogenous Retroviruses Are Abundant and Extensive In Teleosts

Abstract

Spumaretrovirus, among retrovirus clades, has an extensive accumulation of evidence for an ancient origin. Recent discoveries indicate that the Spumaretrovirus ancestor could have been the first retrovirus to appear during the evolution of vertebrates. If they indeed appeared in ancient marine environments hundreds of millions of years ago, we should expect significant undiscovered diversity of foamy-like endogenous retroviruses in fish genomes. I report the discovery of these elements in 23 novel teleost hosts. These viruses have very large genomes compared to all other retroviruses, possess an unprecedented array of accessory genes, and form a robust reciprocally monophyletic sister clade with sarcopterygian host foamy viruses, with class III mammal endogenous retroviruses being the immediate sister group to both clades. I estimated that some of these viruses integrated recently into host genomes, and exogenous descendants of these viruses may be extant.