A compendium of 3,562 human and animal papillomavirus genomes

Papillomaviruses (PVs) are a ubiquitous group of DNA viruses that infect a wide range of vertebrate hosts, including human. It is well established that the infection of some PV types (e.g., HPV16 and HPV18) are strongly associated with the occurrence and progression of cancers in human, but it remains elusive how such pathogenicity got evolved at the genomic level. In this study, we curated and annotated a compendium of 3,562 PV genomes (including 3,329 human PVs and 233 animal PVs) and performed the largest ever comparative genomics analyses on PVs with regard to their global and taxonomical distribution, host and niche specificity, population and phylogenetic stratification, as well as gene repertoire and genetic variants, especially those contribute to PVs' pathogenicity.