The skull bones of a man buried in Latvia around 5,000 years ago. Scientists have determined he had an early version of the plague.
Dominik Goldner, BGAEU, Berlin

A hunter-gatherer who lived 5,000 years ago may have died from an ancient strain of the bubonic plague that killed millions in Europe, Asia and Africa many years later, say scientists who extracted DNA from the man’s teeth and bones.

The researchers believe that man, known as “RV 2039,” harbored the oldest known strain of Yersinia pestis, the bacteria that causes the plague. They say understanding the pathogen’s evolution could shed light on our understanding of human civilization’s development in parts of the world devastated during the gruesome 14th century pandemic known as the Black Death.

“Different pathogens and the human genome have always evolved together,” said Ben Krause-Kyora, head of the Ancient DNA Laboratory at German’s University of Kiel and co-author of a new study detailing the discovery. “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.”

Almost 700 years after the Black Death devastated Eurasia and North Africa, it lives on as a chilling worst-case scenario of pandemic destruction, with its origins continuing to enthrall scientists. The bubonic plague caused a host of symptoms, including fever, chills, headaches, skin sores that form black scabs, and painful swollen and pus-filled lymph nodes known as “buboes” in the armpit or groin. Today, antibiotics can treat the life-threatening infection, but in the Middle Ages, it was all too often a death sentence.

The study, published Tuesday in the journal Cell Reports, reveals the earlier strain was likely less virulent, and less contagious, than the one that killed an estimated 75 million to 200 million people during the Black Death, also known as the Pestilence or Great Mortality.

“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.”

The 5,000-year-old version, the researchers found, lacked the gene that first let fleas act as illness-spreading vectors. Instead, the illness probably spread via a bite from an infected animal. (Notably, perhaps, beavers were a frequent archaeozoological find at the site where RV 2039 was excavated and commonly carried a bacterium that preceded the early Y. pestis.)

The researchers found Y. pestis in RV 2039’s bloodstream and believe he died from an infection caused by the bacteria, but it appears the disease progressed slowly. As Krause-Kyora noted, even a small shift in genetic configurations can have a dramatic impact on virulence.

“Understandably there are no clinical studies that have looked at the ability of the strain to cause disease, and therefore whether it could be epidemic or pandemic proportions,” said Sian Halcrow, a bioarchaeology professor at the University of Otago in New Zealand who is not affiliated with the study. “However, it gives us an important glimpse into the emergence and evolution of the Black Death.”

The skeleton of RV 2039 — who is believed to have been between 20 and 30 when he passed — was among those excavated in the late 1800s at Rinnukalns, a Neolithic shell dump in Northern Latvia. Krause-Kyora and fellow European researchers used samples from his teeth and bone to sequence his genome and test it for bacterial and viral pathogens. They detected three Y. pestis-specific proteins in the DNA sample.

The new study comes as scientists and others scramble to understand the origins of the modern-day COVID-19 pandemic in an attempt to prevent another one.

“By studying the interactions between pathogens, humans, animals and changes in society, demography and the environment,” Halcrow said, “we can better understand present-day disease outbreaks.”