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Earliest known strain of plague could have come from a beaver bite

The skull of the hunter-gatherer, who has been dubbed RV 2039.
The skull of the hunter-gatherer, who has been dubbed RV 2039. (Image credit: Dominik Goldner, Bgaeu, Berlin)

Scientists have found the earliest known strain of plague in the remains of a 5000-year-old hunter gatherer. 

The "astonishing" discovery pushes back the first appearance of the plague bacterium (Yersina Pestis) by more than 2,000 years, study senior author Ben Krause-Kyora, a biochemist and archaeologist at the University of Kiel in Germany said in a statement. This date is probably close to when the bacteria first evolved, he added.

The plague-carrying hunter-gatherer, dubbed "RV 2039", was a 20- to 30-year-old man and one of four people whose remains were excavated from a burial site near the Baltic Sea in Latvia. An analysis of samples from the man’s teeth and bones revealed that he was likely the only one among those buried with the disease. Researchers reconstructed the bacteria’s genome using genome sequencing, and believe the bacteria was likely a part of a lineage that emerged roughly 7,000 years ago, not long after Yersina Pestis split from a predecessor, Yersina pseudotuberculosis.

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The analysis also revealed that most of the deadly disease’s key genes were already in place, even at this early stage of its history. "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. But even a small shift in genetic settings can have a dramatic influence on virulence," Krause-Kyora said.

Modern plague variants contain one important thing that the newly-discovered ancient strain lacked — a gene enabling fleas to carry the disease. This adaptation hugely increased the rate at which the plague bacteria could infect human hosts, entering the body and travelling to the lymph nodes where it would rapidly replicate. The host would then form painful, pus-filled buboes — from which the bubonic plague gets its name — on their skin. 

But the switch to fleas as a means of transmission required the disease to kill its host: an old host’s death encourages fleas to move to a new host and pass on the disease. The researchers speculate that this new gene was responsible for driving  the plague to become deadlier.     

Because this early strain of Y. pestis was not yet flea-borne, the scientists think that the bacteria originally entered the hunter-gatherer’s body through a rodent bite, possibly from a beaver, a common carrier of the plague predecessor Y. pseudotuberculosis and the species with the most remains recorded at the site. Once there, the course of the disease was fairly slow, with bacteria slowly accumulating in high quantities in the man’s bloodstream until he died.

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The three pandemics the bacteria would go on to cause are among the deadliest biological events in human history. The first pandemic, the Justinian Plague (which occurred roughly between A.D. 542 and 750), may have caused the Mediterranean population to decline by 40% by the end of the sixth century. The second, and most infamous, pandemic caused by the disease was the 14th century European Black Death, which killed approximately 25 million people — between 33 to 50% of Europe’s population. A third, lesser known, pandemic began in 1855 in China’s Yunnan province and killed more than 12 million people in India and China alone.

The people buried around RV 2039 were not infected and he was carefully placed in his grave, two indications that he didn’t carry the later, highly-contagious version of the disease. But because of its presence in his blood, scientists still think the plague bacteria could have killed him. 

The idea that this ancient bacteria replicated slowly and was passed from rodent to human is bolstered by the fact that scientists have found other ancient skeletons infected with Y. pestis at other sites, where people lived very different lifestyles. "Isolated cases of transmission from animals to people could explain the different social environments where these ancient diseased humans are discovered. 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 occurrences of Y. pestis cases," Krause-Kyora said.

The picture of the early plague as a slow-acting, less virulent disease raises serious challenges to theories about the development of civilization in Europe and Asia.

One of these theories is that the plague was the cause of large declines in Western European populations towards the end of the Neolithic Age. In 2019, a tomb in modern-day Sweden containing 78 hastily buried bodies was dated to roughly the same period as RV 2039, and one set of bones and teeth, belonging to a woman also contained plague bacteria fragments, Live Science previously reported.  

In fact, remains containing traces of plague bacteria have been found in sites all across Eurasia, and dated to coincide with the rapid decline in Neolithic populations between five and six thousand years ago.

Another theory is that the plague evolved in European "mega settlements" containing 10,000 to 20,000 people which existed between 6,100 and 5,400 years ago. But the new research suggests Y. Pestis could have split from Y. pseudotuberculosis as far back as 7400 years ago, a time when European populations had yet to grow beyond collections of sparse settlements. 

The mystery of this population collapse, and whether it was caused by an early form of plague, has yet to be fully unravelled. The researchers believe that their work could open further investigation into the history of plague, offering valuable insights not just on the evolution of the disease, but on early human history and genomics.

"Different pathogens and the human genome have always evolved together. 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," Krause-Kyora said. "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."

Their findings were published June 29 in the journal Cell Reports.

Originally published on Live Science.

Ben Turner is a U.K. based staff writer at Live Science. He covers physics and astronomy, among other topics like weird animals and climate change. He graduated from University College London with a degree in particle physics before training as a journalist. When he's not writing, Ben enjoys reading literature, playing the guitar and embarrassing himself with chess.