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International Team of Scientists Use Genetic Testing to Solve Centuries-Old Mystery of Black Death’s Origin

DNA analysis of early plague victims pinpoints Black Death’s start on Silk Road trading communities in mountain region of what is now modern-day Kyrgyzstan in Central Asia

Microbiologists and clinical laboratory scientists will likely find it fascinating that an international team of scientists may have solved one of history’s greatest mysteries—the origin of the bubonic plague that ravaged Afro-Eurasia in the mid fourteenth century. Also known as the Black Death, the plague killed 60% of the population of Europe, Asia, and North Africa between 1346-1353 and, until now, the original source of this disease has largely gone unsolved.

Using DNA analysis and archeological evidence, a multidisciplinary team of scientists from the Max Planck Institute for Evolutionary Anthropology in Germany, the University of Tubingen in Germany, and the University of Stirling in the United Kingdom traced the pandemic’s origin to North Kyrgyzstan in Central Asia in the late 1330s.

In their study published in the journal Nature, titled, “The Source of the Black Death in Fourteenth-Century Central Eurasia,” the authors outlined their investigation of cemeteries in the Chüy Valley of modern-day Kyrgyzstan. The tombstone inscriptions showed a disproportionally high number of burials dating between 1338 and 1339 with inscriptions stating “pestilence” as the cause of death.

Johannes Krause, PhD
Archeological evidence combined with ancient DNA analysis of early plague victims enabled scientists to pinpoint the Black Death’s origins in Kyrgyzstan. “We have basically located the origin in time and space, which is really remarkable,” geneticist Johannes Krause, PhD (above), Professor at the Max Planck Institute for Evolutionary Anthropology, who co-led the study, told The Guardian. “We found not only the ancestor of the Black Death, but the ancestor of the majority of the plague strains that are circulating in the world today.” These new research findings may help microbiologists and clinical pathologists gain new insights into how current strains of Yersinia pestis can be better diagnosed. (Photo copyright: Max Planck Institute.)

Big Bang of Plague

Using 30 skeletons that were excavated from these cemeteries in the late 1880s and moved to St. Petersburg, Russia, the scientists analyzed the DNA of ancient pathogens recovered from the remains of seven people. They discovered Yersinia pestis (Y. pestis) DNA in three burials from Kara-Djigach, which lies in the foothills of the Tian Shan mountains.

According to another article in Nature, the scientists showed that a pair of full Y. pestis genomes from their data were direct ancestors of strains linked to the Black Death, and that the Kara-Djigach strain was an ancestor of the vast majority of Y. pestis lineages circulating today.

“It was like a big bang of plague,” Krause stated at a press briefing, Nature reported.

The research team concluded that the Tian Shan region was the location where Y. pestis first spread from rodents to people, and that the local marmot colonies likely the prevalent rodent carriers of plague.

“We found that modern strains [of the plague] most closely related to the ancient strain are today found in plague reservoirs around the Tian Shan mountains, so very close to where the ancient strain was found. This points to an origin of Black Death’s ancestor in Central Asia,” Krause explained in a Max Planck Institute news release.

He told Nature that fleas likely passed the marmot-based infection on to humans, sparking a local Kyrgyzstan epidemic. The disease then spread along the Silk Road trade routes, eventually reaching Europe, where rats (and the fleas that they carried) spread the disease. 

Understanding Context of Plague

Writing in The Conversation, Associate Professor of Medieval and Environmental History Philip Slavin, PhD, University of Stirling, who co-authored the study, explained that Kara-Djigach is unlikely to be “the specific source of the pandemic,” but rather that the “disaster started somewhere in the wider Tian Shan area, perhaps not too far from that site,” where marmot colonies were likely the source of the 1338-1339 outbreak.

Making a modern-day comparison, Krause told Nature, “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.”

Slavin maintains that understanding the “big evolutionary picture” is key when studying the phenomenon of emerging epidemic diseases.

“It is important to see how these diseases develop evolutionary and historically, and avoid treating different strains as isolated phenomena,” he wrote in The Conversation. “To understand how the diseases develop and get transmitted, it is also crucial to consider the environmental and socioeconomic contexts.”

Scientists have spent centuries debating the source of the Black Death that devastated the medieval world. The multidisciplinary process used by the Slavin/Krause-led team provides a lesson to clinical laboratory managers and pathologists on the important role they play when collaborating with colleagues from different fields on scientific investigations.   

Andrea Downing Peck

Related Information:

Mystery of Black Death’s Origins Solved, Say Researchers

Black Death: How We Solved the Centuries-Old Mystery of Its Origins

Ancient DNA Traces Origin of Black Death

The Source of the Black Death in Fourteenth-Century Central Eurasia

Origins of the Black Death Identified

Researchers in Germany Sequence Genome of Bubonic Plague Bacteria Taken from Remains of Man who Lived More than 5,000 Years Ago

Advancements in genetic sequencing continue to enable microbiologists and genetic scientists to explore the origins and mutations of deadly diseases

Microbiologists and researchers can now study the gene sequence of 5,000-year-old bubonic plague bacteria. The scientific team that achieved this feat of gene sequencing believes this is the oldest case of the ancient strain of the plague found to date.

Scientists working at the Institute of Clinical Molecular Biology (IKMB) at the Kiel University and the Centre for Baltic and Scandinavian Archaeology (ZBSA) in Germany, and at the Institute of Latvian History (LVI) at the University of Latvia, recently found remnants of Yersinia Pestis, the infectious bacterium that causes the bubonic plague, in the jawbone of a man who lived more than 5,000 years ago.

For microbiologists, this demonstrates how advances in gene sequencing technologies are allowing scientists to go further back in time to look at how the genomes of bacteria and viruses have evolved and mutated. This helps science understand the process of genetic mutation, as well as learning which mutations survived because they could more easily infect humans.

The scientists published their findings in the peer-reviewed journal Cell Reports, titled, “A 5,000-Year-Old Hunter-Gatherer Already Plagued by Yersinia Pestis

Missing Gene has ‘Dramatic Influence on Virulence’ of Plague

To conduct their study, the researchers sequenced the genomes of samples from the teeth and bones of four hunter-gatherers and tested the remains for bacterial and viral pathogens. They found evidence of Yersinia pestis (Y. pestis) in the dental remains of a 20- to 30-year-old male dubbed RV 2039.

The jaw bones used for the research were discovered in the late 1800s in the Rinnukalns, a stone age settlement unearthed in present-day Republic of Latvia in the late 19th century.

Missing Genetic Element in Ancient Bacterium

The scientists were surprised to find evidence of Y. pestis in the remains and noted that the analysis of the microbe lacked a crucial genetic element observed in later strains of the bacteria. Missing was the gene that allows biting fleas to act as vectors to spread the plague to humans.

“What’s so surprising is that we see already in this early strain more or less the complete genetic set of Y. pestis, and only a few genes are lacking,” said biochemist and archeologist Ben Krause-Kyora, Professor and head of the Ancient DNA (aDNA) Laboratory at the University of Kiel in Germany, and one of the authors of the study, in a press release.

“But even a small shift in genetic settings can have a dramatic influence on virulence,” he added.

This absent gene also is responsible for creating the pus-filled buboes associated with the Black Death (bubonic plague) that occurred in the 1300s. The Black Death killed 75 million to 200 million people worldwide, mostly in Eurasia and North Africa. It is to date the most fatal pandemic recorded in human history.

Professor Ben Krause-Kyora and colleagues

“Different pathogens and the human genome have always evolved together,” said Professor Ben Krause-Kyora (above left with and Steve Zäuner at center and Dr. Silvia Codreanu-Windauer at right), in the press release. “We know Y. pestis most likely killed half of the European population in a short time frame, so it should have a big impact on the human genome. But even before that, we see major turnover in our immune genes at the end of the Neolithic Age, and it could be that we were seeing a significant change in the pathogen landscape at that time as well,” he added. (Photo copyright: Mittelbayerische.)

A Less Lethal Bubonic Plague?

Although RV 2039 most likely perished from the bubonic plague, the researchers believe his strain of the infection was more mild, less contagious, and not as lethal as the later genetic mutations of the bacteria that caused the Black Death pandemic. The researchers concluded that the man most likely contracted the disease through a bite from an infected rodent or other animal, the press release notes.

“Isolated cases of transmission from animals to people could explain the different social environments where these ancient diseased humans are discovered,” Krause-Kyora said in the press release. “We see it in societies that are herders in the steppe, hunter-gatherers who are fishing, and in farmer communities—totally different social settings but always spontaneous occurrence of Y. pestis cases.”

From Animal Bite to Flea Infection in 7,000 Years’ Worth of Mutations

The Y. pestis bacteria that infected RV 2039, the researchers surmised, most likely split from its predecessor, Yersinia pseudotuberculosis, which first appeared on Earth about 7,000 years ago. It most likely took Y. pestis over a thousand years to acquire all the mutations necessary for flea-based transmission of the bacteria to humans, the researchers noted.

“What’s most astonishing is that we can push back the appearance of Y. pestis 2,000 years farther than previously published studies suggested,” Krause-Kyora said. “It seems that we are really close to the origin of the bacteria.”

It is unknown how many cases still occur worldwide due to unreliable diagnoses and poor reporting in developing countries. However, data from the World Health Organization (WHO) states that there were 3,248 cases of plague reported worldwide between 2010 and 2015, including 584 deaths. Currently, the three most endemic countries for plague are the Democratic Republic of the Congo, Madagascar, and Peru.

The researchers’ findings illustrate how advances in gene sequencing technologies are helping microbiologists, virologists, and genetic scientists understand the affect mutations have on diseases that have plagued humans since the beginning of humanity itself.

Will this lead to new genomic diagnostics? Perhaps. The research is worth watching.

—JP Schlingman

Related Information

What a 5,000-year-old Plague Victim Reveals about the Black Death’s Origins

A 5,000-year-old Hunter-gatherer Already Plagued by Yersinia Pestis

This 5,000-year-old Man had the Earliest Known Strain of Plague

Five Things You Might Not Know about the Plague (Not Including the Fact That it Still Exists)

Plague: Frequently Asked Questions

Plague: Key Facts