More than six centuries ago, the Black Death ravaged Europe, Asia, and North Africa. The plague killed up to 60 percent of the people in western Eurasia within eight years. How the bacterial strain responsible for this pandemic infiltrated human populations has been debated ever since.

In a study published on June 15 in Nature, an international group of researchers pinpoints the Black Death’s ground zero to early 14th-century Central Asia. They analyzed historical records, archaeological data, and DNA from the teeth of skeletons buried in two cemeteries in Kyrgyzstan. Within those 700-year-old remains, the scientists identified the plague-causing bacterium, Yersinia pestis

The team concluded that the pandemic germ’s ancestor evolved in this area, based on its relationship to present-day strains of Y. pestis. The findings solve a centuries-old mystery and can also help understand emerging infectious diseases, Philip Slavin, a historian at the University of Stirling in Scotland and co-author of the findings, told Popular Science in an email. 

“It’s always important to not treat different strains as isolated phenomena,” he said, “but as something that is situated within a much wider evolutionary picture.”

Experts who weren’t involved with the study say the results are intriguing but require more confirmation.

“[The] findings are interesting but preliminary, and further research is desirable and required to enlarge and deepen the findings,” Ole J. Benedictow, an emeritus professor of archaeology, conservation, and history at the University of Oslo in Norway and author of The Complete History of the Black Death, said in an email. “Paleobiological historical plague studies are still in an early phase of development, we can expect a wealth of new interesting findings and many surprises in the future.” 

Finding plague in teeth

Infected fleas, whose rodent hosts have perished, typically transmit plague to people. Y. pestis has afflicted humans for more than a millenium, causing three separate pandemics that began in the 6th, 14th, and 19th centuries. The Black Death took place between 1346 and 1353; after this initial devastating wave, the bubonic plague settled into a pandemic that lasted for several centuries.

Scholars—including scientists from the 14th century and modern historians—have speculated about many potential locations for the Black Death’s initial source. Those sites have included China, Central Asia, the steppes between the Black and Caspian Seas, Mongolia, Russia, and India, Slavin said. 

To trace its origin, Slavin and his collaborators examined the remains from two cemeteries near Lake Issyk-Kul in present-day Kyrgyzstan. The cemeteries had been excavated during the late 19th century but are much older: Tombstone inscriptions dated from 1338 to 1339 state that a number of the bodies had been victims of “pestilence.” To verify the identity of that pestilence, the team extracted genetic material from the teeth (which preserve the pathogens present in a person’s bloodstream) of seven individuals. They detected Y. pestis in three people from the Kara-Djigach cemetery. 

Archaeology photo
The Kara-Djigach site, excavated between 1885 and 1892, and photographed here in 1886.  A.S. Leybin

While the DNA had broken down over time, two of the teeth contained enough material for the team to reconstruct the bacterial strain’s position within the plague family tree. The researchers concluded that the strain of Y. pestis in the teeth was the most recent common ancestor of several branches of plague still found today, one of which included the strain responsible for the Black Death. Additionally, the team reported, the ancient Kara-Djigach strain is closely related to the Y. pestis that continues to circulate in marmots of the surrounding Tian Shan mountains. 

“We consider [it] most probable that the ancient strain evolved locally, within the extended Tian Shan Mountain region, and was not introduced into the Kara-Djigach community from a far-away source,” Slavin said. “At some point the bacteria crossed over from marmots to humans.”

The presence of gems, silks, coins, and other artifacts near the cemeteries indicate that the communities struck by the epidemic contained many goods that had been produced far away. Trade may have played an important role spreading the pathogen westward to the Black Sea, Slavin said in a call with reporters. 

An unsettled genesis

The new report confirms that the pestilence victims near Lake Issyk-Kul did indeed die of plague, said Nükhet Varlık, a medical historian at Rutgers University–Newark who wasn’t involved in the research. However, this doesn’t necessarily establish the source of the Black Death. “Here we are presented with one plausible origins scenario, but it does not exclude other possible ones,” Varlık said in an email. 

Many questions remain concerning the paper’s “larger implications” for the history of the Black Death and the pandemic it kicked off, she said. Among these are what conditions could have prompted the disease to spill from local rodents into people near Lake Issyk-Kul, or whether the infection might have instead been introduced from elsewhere. 

“Moreover, we still do not know how this local outbreak was historically connected to the earliest recorded incidence of the Black Death in the Black Sea region in 1346,” Varlık said. “Evolutionary studies of Yersinia pestis and our modern experience with the COVID-19 pandemic teach us that it may be nearly impossible to establish [the] ‘true origin’ of pandemics.”

[Related: You could get the plague (but probably won’t)]

The new findings suggest that the ancestor of the Black Death strain showed up considerably later than previous work has indicated, said Vladimir Motin, a microbiologist at the University of Texas Medical Branch at Galveston who studies Y. pestis. Earlier studies suggested it caused local outbreaks in Asia for at least a century, he said.

“Right now it’s a good hypothesis; is it true or not, I don’t know,” he said. “But it’s definitely an interesting question which we should take into consideration.”

Monica H. Green, an independent scholar who specializes in medical and medieval history, agrees with Varlık that the paper establishes 14th-century remains in Kyrgyzstan were infected with Y. pestis. But Green, who has studied the presence of plague in western Asia in the 1250s, isn’t convinced the findings determine the time period when this ancestral strain appeared. The plague bacterium mutates slowly when it’s circulating in marmots, she points out, which means that the strain might have made its debut well before the outbreaks.

“Have they documented emergence of a new stage in plague’s history…in the 14th century?” Green said in an email. “Or have they documented the persistence of a new lineage that had already been dispersing for several decades by the time these two communities to the west of Issyk-Kul were struck?” 

She suspects that the strain Slavin and his team retrieved is a “cousin” of the bacteria that spread westward to cause the Black Death. To unravel the pandemic’s genesis, researchers will need to collect more ancient DNA samples from the region and beyond. 

The history of plague offers important clues toward understanding how pandemics begin and spread, Green said. “We have never needed rigorous debate about pandemic histories more than now.”