A team of Spanish researchers studying HPV epidemiology have found evidence to suggest that a main clade of the virus originated as an infection of Neanderthals.
HPV16, which is a particularly carcinogenic strain of the virus, is the main type of HPV in Eurasia the Americas. Coincidentally, the strain is all but completely absent on the African continent. Researchers used statistical analysis to determine that the strain left Africa with Neanderthals and Denisovans sometime before the appearance and global spread of Homo sapiens. Strains of HPV found on the African continent are related to, but distinct from HPV16, and reflect a historic diversity of HPV strains on that continent, largely reflective of humanity's origin on the African continent.
How HPV16 jumped between species? A lot of inter-species sex.