It devastated cities, stalled the growth of empires, and shuffled the leadership of royal houses like a handful of playing cards. A historian called it “the most terrible of all the ministers of death.”
Smallpox was stealthy and relentless, disfiguring and deadly, so traumatizing that it was the first disease for which a vaccine was sought and achieved, and the first that humankind eradicated.
It was the most feared illness in history—but now an achievement of molecular genetics is raising questions about whether our understanding of that history is correct.
A multinational team of researchers, headed by a group at the DeGroote Institute for Infectious Disease Research at McMaster University in Ontario, have retrieved and sequenced smallpox DNA from the mummified body of a child interred in Lithuania in the 17th century. (See pictures of the other mummies found in the Lithuanian crypt.)
Comparing that genetic material with modern smallpox samples, they found them to be surprisingly alike. And by constructing a “molecular clock” that traces the strains’ evolution back to a common ancestor, they dated the virus’s time line no further back than about 1588.
Based on their results, reported this week in the journal Current Biology, the researchers think it’s possible those earlier accounts are misidentifications of other pox-like diseases, and that more ancient samples are needed to affirm or disprove smallpox’s history.
The study of ancient DNA is familiar territory for the group that led the research. The team is led by Hendrik Poinar, who previously reconstructed woolly mammoth DNA and retrieved the genomes of plague bacteria from the teeth of sixth-century skeletons. (He is also the son of the scientist whose work extracting cellular structures from insects preserved in amber inspired Jurassic Park).
But the team did not start the study in pursuit of smallpox; that was a surprise. The work began with the opportunity to extract tissues from an unusual set of mummies that are preserved in a church in Vilnius, Lithuania, which are the study project of Dario Piombino-Mascali, a physical anthropologist who is a National Geographic Explorer.
“These are completely natural mummies, in the sense that no process was carried out to dry them,” says Piombino-Mascali, a visiting researcher at Vilnius University.
“There are 23 with good to excellent preservation of soft tissue. Seven are intact, so we have only CT-scanned them. But the ones that have some loss of substance or are missing some body part, we sampled the soft tissue from them.”
The first tissue Piombino submitted to Poinar’s lab was from a preserved partial body: the pelvis and legs of a child whom the team estimate to have been 2 to 4 years old when he or she died, sometime between 1643 and 1665.
There were no signs of illness, including no visible pustules, on the preserved limbs. The lab extracted and sequenced the genetic material in the sample, intending to look for an organism called JC polyomavirus that is a research interest of one of the team members.
To their surprise, out of the stew of genetic material in the sample, they got more than 200 matches that indicated fragmentary, damaged, and non-infectious smallpox DNA.
After further work, the team pulled out and reassembled the entire genome of Variola, the viral cause of smallpox, and then compared it to records of other smallpox samples. The oldest external sample came from 1944 and the latest from 1977, just before the disease was declared eradicated.
Because the modern samples had precise dates of collection, the team was able to use them to measure the degree of evolutionary difference between them, as well as the divergence between the modern samples and the 17th century one, and to predict a consistent rate at which the virus changed.
“We can move backward through time and build the evolutionary process in reverse,” says Ana Duggan, the paper’s first author and a post-doc at the DeGroote Institute.
At the other end of that process, they arrived at a date for a single common ancestor where the evolutionary differences would converge. That date is between 1588 and 1645. If correct, the finding would confirm that smallpox was responsible for the terrible epidemics that made it notorious—but exonerate it from responsibility for the millennia-old cases described in archives.
Crucially, the diversity of the viral genomes the group studied “isn’t particularly high,” Duggan notes.
“If you are going to follow this historical narrative that smallpox is thousands of years old—whether you say that smallpox begins with 2,000-year-old mummies, or extrapolate back and say smallpox has been with us since the dawn of agriculture—you might expect there would be a lot more diversity, and we don’t see that.”
In their paper, the team says there may be historical evidence to back this revised time line. For instance, municipal “bills of mortality” listing deaths only begin to mention severe smallpox in 1632. And other related diseases, such as cowpox and monkeypox, cause similar pustular rashes. (An outbreak of monkeypox spread by exotic pets caused a bioterrorism scare in the Midwest in 2003.)
Though it was eradicated from the planet, smallpox is not quite dead; samples of the virus remain under containment at the U.S. Centers for Disease Control and Prevention and in Russia. It is considered an agent of bioterrorism—and as such, there are few researchers who work with it.
One of the deans of smallpox research, Inger Damon of the CDC, said by email that the paper “impressively demonstrates advances in methods to obtain genomic information from ancient biologic materials. The authors have a number of useful insights about the application of molecular ‘dating’ methods.”
The team hopes to push their work further, but that may be an uphill battle: Little of the research done so far on ancient DNA has targeted viruses, so there is not much with which to compare their work. And smallpox genomes are understandably scarce.
“We’re especially interested in trying to find early 16th-century samples from the New World; smallpox transmitted by Europeans was implicated in the downfall of Native American societies,” Duggan says. “If we had older strains, maybe we could build a totally different picture.”