Abstract
Endogenous retroviruses (ERVs) represent host genomic fossils of ancient viruses. Foamy viruses, including those that form endogenous copies, provide strong evidence for virus-host co-divergence across the vertebrate phylogeny. Endogenous foamy viruses (EFV) have previously been discovered in mammals, amphibians and fish. Here we report a novel endogenous foamy virus, named SpuEFV, in genome of the tuatara (Sphenodon punctatus), a reptile species endemic to New Zealand. Surprisingly, SpuEFV robustly grouped with the coelacanth EFV on virus phylogenies, rather than with the mammalian foamy viruses as expected with virus-host co-divergence, and indicative of a major cross-species transmission event in the early evolution of the foamy viruses. In sum, the discovery of SpuEFV fills a major gap in the fossil record of foamy viruses and provides important insights into the early evolution of retroviruses.