A reptilian endogenous foamy virus sheds light on the early evolution of retroviruses

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 (EFVs) have previously been discovered in mammals, amphibians, and fish. Here we report a novel endogenous foamy virus, termed ERV-Spuma-Spu, in genome of the tuatara (Sphenodon punctatus), an endangered reptile species endemic to New Zealand. Phylogenetic analyses revealed that foamy viruses have likely co-diverged with their hosts over many millions of years. The discovery of ERV-Spuma-Spu fills a major gap in the fossil record of foamy viruses and provides important insights into the early evolution of retroviruses.