Broad-scale phylogenomics provides insights into retrovirus–host evolution

Significance Retroviruses, such as HIV, are important pathogens of vertebrates, including humans. They are capable of crossing species barriers to infect new hosts, but knowledge about the evolutionary history of retroviruses is limited. However, genomic traces of past retrovirus activities known as “endogenous retroviruses” can be screened from sequenced genomes and analyzed to improve understanding of retrovirus evolution. Here we use a unique approach to address the evolution of one group of retroviruses in a screen of 60 diverse vertebrate host genomes. We find evidence of rampant host-switching across mammalian orders by members of this group throughout their evolutionary history. We also find evidence that the spread of infective retroviruses from this group may be facilitated by rats.