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Ancient DNA traces origin of Black Death

An engraved tombstone of a victim of the black death recovered from the Kara-Djigach burial site in modern-day Kyrgyzstan

An engraved tombstone of a person who died from the Black Death plague, from the Kara-Djigach cemetery in what is now Kyrgyzstan.Credit: P.-G. Borbone, M. A. Spyrou et al./Nature

A Silk Road stopover might have been the epicentre of one of humanity’s most destructive pandemics.

People who died in a fourteenth-century outbreak in what is now Kyrgyzstan were killed by strains of the plague-causing bacterium Yersinia pestis that gave rise to the pathogens responsible several years later for the Black Death, shows a study of ancient genomes.

“It is like finding the place where all the strains come together, like with coronavirus where we have Alpha, Delta, Omicron all coming from this strain in Wuhan,” says Johannes Krause, a palaeogeneticist at the Max Planck Institute for Evolutionary Anthropology in Leipzig, Germany, who co-led the study, published on 15 June in Nature1.

Between 1346 and 1353, the Black Death laid waste to western Eurasia, killing up to 60% of the populace in some places. Historical records suggest that the bubonic plague emerged from the east: Caffa, on the Crimean peninsula, experienced one of the earliest-recorded outbreaks of plague during a 1346 siege by the army of the Mongol Empire. The Caucasus and other locales in Central Asia have been put forward as potential epicentres.

China hosts some of the world’s greatest genetic diversity of modern Y. pestis strains, hinting at an East Asian origin for the Black Death. “There were all kinds of hypotheses in the literature. And it was not really known where it exactly came from,” says Krause.

Signs of the plague

Several years ago, Philip Slavin, an economic and environmental historian at the University of Stirling, UK, and a co-lead author of the study, came across records from a pair of fourteenth-century cemeteries in Kyrgyzstan that, he thought, might hold clues to the origins of the Black Death. The cemeteries, known as Kara-Djigach and Burana, held an unusually high number of tombstones dated to 1338 and 1339, ten of which made explicit reference to a pestilence.

“When you have one or two years with excess mortality, it means something funny is going on there,” Slavin said at a press briefing.

To determine whether the burials held any relevance to the later Black Death, Slavin worked with Krause to track down the remains from the Kyrgyz cemetery — which had been excavated in the 1880s and 1890s and moved to St Petersburg, Russia. The team, led by archaeogeneticist Maria Spyrou at the University of Tübingen, Germany, sequenced ancient DNA from seven people whose remains were recovered, discovering Y. pestis DNA in three burials from Kara-Djigach.

Lanscape showing the Tian Shan mountains in Kyrgyzstan

The Tian Shan mountain range, where researchers have found modern strains of plague-causing bacteria related to the ancient ones from Kyrgyzstan.Credit: Lyazzat Musralina

A pair of full Y. pestis genomes gleaned from the data showed that the bacteria were direct ancestors of strains linked to the Black Death, including a Y. pestis sample from a person who died in London that Krause’s team sequenced in 2011. The Kara-Djigach strain was also an ancestor of the vast majority of Y. pestis lineages around today — a sign, Krause says, of an explosion in Y. pestis diversity shortly before the Black Death. “It was like a big bang of plague,” he said at the press briefing.

Other evidence puts the origins of the Black Death in this part of Central Asia. Among modern strains of Y. pestis bacteria, those sampled from marmots and other rodents in Kyrgyzstan, Kazakhstan and Xinjiang in northwest China, surrounding the Tian Shan mountain range, were most closely related to the Kara-Djigach strain. “We can’t really say it’s that village or that valley, but it’s likely that region,” says Krause.

Rodents are the natural reservoir for Y. pestis, and humans develop bubonic plague only when a vector such as a flea passes on the infection. Krause suspects that humans’ close contact with infected marmots sparked the Kyrgyzstan epidemic, whereas immunologically naive rat populations in Europe fuelled the Black Death.

Tian Shan makes sense as an epicentre for the Black Death, says Slavin. The region is on the ancient Silk Road trade route, and the Kyrgyzstan graves were found to contain pearls from the Indian Ocean, corals from the Mediterranean and foreign coins, suggesting that faraway goods passed through the area. “We can hypothesize that trade, both long distance and regional, must have played an important role in spreading the pathogen westward,” Slavin said.

Medieval ‘death certificates’

Obtaining genomes from plague bacteria ancestral to those behind the Black Death is “a tremendous breakthrough”, says Monica Green, a medieval historian and independent scholar in Phoenix, Arizona. “The headstones are as close as we will ever come to ‘death certificates’. So we know this lineage of Y. pestis was in existence then.” But she’s less sure of the study’s conclusion that the plague’s ‘big bang’ occurred around the time of the Kyrgyzstan deaths in 1338–39. Green has hypothesized, on the basis of genetic, ecological and historical evidence, that the thirteenth-century expansion of the Mongol Empire catalysed the spread and diversification of Y. pestis strains responsible for the later Black Death.

Sharon Dewitte, a bioarchaeologist at the University of South Carolina in Columbia, says the work opens the doors to studying the Black Death — and the wider outbreak it was part of, known as the second plague pandemic — beyond Europe. She’s keen to compare demographic and mortality patterns from people who died of the plague in Kara-Djigach with those from European Black Death cemeteries.

“Having more plague samples from ancient Asia and China will be super interesting in terms of adding even more evidence to the Asian origin of the first and second [plague] pandemics,” adds Simon Rasmussen, a computational biologist at the University of Copenhagen who has analysed ancient Y. pestis sequences.

Krause hopes to analyse remains from China to see how a pandemic that so scarred Europe reverberated in East Asia, he says. “We would really like to get the Eastern part of the story.”

Nature 606, 635-636 (2022)


Updates & Corrections

  • Clarification 16 June 2022: This story has been updated to make clear that Monica Green used ecological and historical evidence, as well as genetic evidence, to reach her conclusions about the spread of the Black Death.

  • Correction 16 June 2022: This story originally quoted Johannes Krause saying “it was really known where it exactly came from”; that should have said “it was not really known where it exactly came from”. The text has been updated.


  1. Spyrou, M. A. et al. Nature (2022).

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