Diverse variola virus (smallpox) strains were widespread in northern Europe in the Viking Age. Ancient variola virus DNA

Smallpox, one of the most devastating human diseases, killed 300–500 million people in the 20th century alone. We recovered viral sequences from thirteen northern European individuals, including eleven from ~600–1050 Common Era, overlapping the Viking Age, and reconstructed near-complete variola virus genomes for four of them. The samples pre-date the earliest confirmed smallpox cases by ~1000 years and the sequences reveal a now-extinct sister clade to the modern variola viruses in circulation prior to the eradication of smallpox. We date the most recent common ancestor of variola virus to ~1700 years ago. Distinct patterns of gene inactivation in the four near-complete sequences show that different evolutionary paths of genotypic host adaptation resulted in variola viruses that circulated widely among humans.