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DNA evidence reveals where the Black Death began

The excavation of the KaraDjigach site, in the Chu-Valley within the foothills of the Tian Shan mountains of Kyrgyzstan, in August 1886. (A.S. Leybin/AFP/Getty Images)

Today, he is known only by the inscription on his burial stone: “This is the tomb of the believer Sanmaq. [He] died of pestilence.”

That brief detail provided a tantalizing clue for historian Philip Slavin, an associate professor at the University of Sterling in Scotland. He wondered if Sanmaq—along with 117 other people buried with him in 1338 and 1339 at cemeteries in what is now northern Kyrgyzstan—could have been killed by the bubonic plague. Emerging in full force in Europe around eight years later, that pernicious pandemic claimed as many as 200 million lives across Europe, Asia and Africa during the 14th century.

“I was almost 100 percent certain it was the beginning of the Black Death,” Slavin told Science magazine

Now DNA research has confirmed his suspicion. Genetic material extracted from seven bodies shows that they had been infected with Yersinia pestis, the bacterium responsible for one of the largest infectious disease catastrophes in human history. This strain started a deluge of death that would devastate human populations for the next 500 years. The plague first reached the United States in 1900, where it killed 119 people during an outbreak in San Francisco.

In a study published Wednesday in the science journal Nature, Slavin and a team of international researchers claim to offer historical proof that Central Asia is where the late medieval bubonic plague actually began.

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“Our study puts to rest one of the biggest and most fascinating questions in history and determines when and where the single most notorious and infamous killer of humans began,” Slavin said in a statement.

The historian said he always had been fascinated by the plague and began to wonder about its origins when he learned of the graves in Kyrgyzstan, a country located north of Afghanistan. The ancient cemetery had been discovered by Russian researchers in 1880s. Remains of 30 individuals had been moved to the Peter the Great Museum of Anthropology and Ethnography in St. Petersburg.

“Despite the risk of environmental contamination and no guarantee that the bacteria would have been able to be preserved, we were able to sequence aDNA (ancient DNA) taken from seven individuals unearthed from two of these cemeteries,” said one of the study’s authors, Maria Spyrou of the University of Tubingen, in a statement. “Most excitingly, we found aDNA of the plague bacterium in three individuals.”

The plague first struck Europe in 1347 from ships sailing on the Mediterranean Sea after appearing beforehand around the Black Sea. It spread quickly, killing an estimated 60 percent of people in Asia, Europe, Middle East and North Africa. It ravaged populations globally for centuries until scientists discovered that fleas borne on rats were responsible for spreading the bacterium.

Initially known as the Plague or the Pestilence, people began to call it the Black Death in the 1750s, primarily because many victims exhibited tissue blackened by gangrene. The disease causes lymph nodes, or buboes—the source of the term “bubonic”—to swell and ooze pus. Most infected people died.

The 14th-century outbreak is remembered today as the Second Plague Pandemic, which followed another deadly disaster, the Great Famine of 1315-1317. The First Plague Pandemic occurred from 541 to 767 and is believed to have been an earlier form of the bacterium.

Researchers and historians have postulated about the origins of the second pandemic since it began. Some believed it started in China and moved westward with the invasions of the Mongol Empire about the same time. This new evidence disputes that theory, though.

In 2011, scientists sequenced the genome of Yersinia pestis from two bodies found in a burial pit in London. Using computer programs, they were able to determine the evolution of the bacterium from earlier versions dating back 5,000 years.

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“Just like COVID, the Black Death was an emerging disease, and the start of a huge pandemic that went on for some 500 years,” another of the study’s authors, Johannes Krause of the Max Planck Institute for Evolutionary Anthropology in Leipzig, said in a statement. “It’s very important to understand actually in what circumstances did it emerge.”

The plague strain eventually evolved into a less lethal variety. Amazingly, the research team discovered that bacterium on wild rodents that still traverse the terrain near Sanmaq’s grave in Kyrgyzstan.

“What’s really remarkable is that today, in the rodents living in that region, we have the closest living relatives of that big bang strain (of plague bacteria),” Krause said at a news briefing. “We found not just the ancestor of the Black Death, but we actually found the ancestor of the majority of plague strains that are circulating in the world today.”