Ancient rashes that scar the faces of Egyptian mummies have long been cited as evidence that smallpox ravaged the region more than 3000 years ago. But now, a study of viral DNA extracted from a 17th century child mummy—the oldest known sample of any virus—suggests that the deadliest form of smallpox emerged in humans much more recently, just in time to hitchhike with New World explorers and decimate populations around the world.

If the team’s analysis is right, it would “challenge many of the current beliefs about one of the most notorious pathogens in human history,” says historian Kyle Harper of the University of Oklahoma in Norman, who was not involved with the work.

The team behind the new study recovered the smallpox virus by accident. Researchers in Lithuania and Finland hoping to gather DNA from a more obscure virus collected tissue from the mummified remains of a young child found within the mid-17th century crypt of the Dominican Church of the Holy Spirit of Vilnius. The child had no visible pox marks, but when the researchers sent the sample to the ancient DNA lab of Hendrik Poinar at McMaster University in Hamilton, Canada, his postdoc Ana Duggan got a big surprise. The sample was rich with variola, the virus that causes smallpox, the team reports today in Current Biology . The large quantity of the virus allowed the researchers to construct a high-quality copy of its genome, the first from such an old virus. (The most ancient pathogens sequenced have been from bacterial DNA, including one that caused the plague 1600 years ago.)

The team was also surprised to find that the child mummy’s ancient viral DNA shared many distinct features with modern strains of the variola virus, including several mutations, suggesting they were closely related. The researchers built a family tree of 49 modern strains and the child’s ancient one, and traced the evolution of all of them back to a common ancestor that arose between 1530 and 1654 C.E.

This date is remarkably recent—only a hundred years or so before the time of the child mummy, and long after the dynasties of Egyptian pharaohs. It’s also much later than other accounts of epidemics, such as pustulous rashes from fourth century China and the Antonine Plague in Rome in 165 C.E., which have been attributed to smallpox by historians. These people may have suffered from chickenpox or measles instead, says Poinar, or from a different type of less deadly pox, which has since gone extinct.

But where did this new, deadly strain of variola come from in the 16th and 17th centuries? One possibility is that it could have lurked in an animal host and jumped to humans. Alternately, a mutation may have arisen in variola in humans that made it more deadly. If it did come from animals, it could still persist there, with the potential of reinfecting humans again, Poinar says.

The study “raises interesting questions about the diversity of strains that were present in the prevaccination era,” says Anne Stone, a biological anthropologist at Arizona State University in Tempe. The first step in solving this mystery will be to replicate the team’s result, says Ann Carmichael, an emeritus historian at Indiana University in Bloomington. She herself scoured death records in Italy and France and could find no real evidence of epidemics of smallpox before the 17th century. Carmichael predicts ancient DNA researchers will embark on a similar quest. “Everywhere there are mummies, they’re going to be looking.”