Ancient DNA provides evidence of 27,000-year-old papillomavirus infection and long-term codivergence with rodents

The long-term evolutionary history of many viral lineages is poorly understood. Novel sources of ancient DNA combined with phylogenetic analyses can provide insight into the time scale of virus evolution. Here we report viral sequences from ancient North American packrat middens. We screened samples up to 27,000-years old and found evidence of papillomavirus (PV) infection in Neotoma cinerea (Bushy-tailed packrat). Phylogenetic analysis placed the PV sequences in a clade with other previously published PV sequences isolated from rodents. Concordance between the host and virus tree topologies along with a correlation in branch lengths suggests a shared evolutionary history between rodents and PVs. Based on host divergence times, PVs have likely been circulating in rodents for at least 17 million years. These results have implications for our understanding of PV evolution and for further research with ancient DNA from Neotoma middens.