Ancient DNA Reveals Lethal Plague Outbreaks 5,500 Years Ago
Plague killed humans 5,500 years ago in hunter-gatherer groups near Lake Baikal, East Siberia, according to a study published in Nature. Researchers found that these early strains of Yersinia pestis were highly lethal, predating the emergence of farming communities and cities by thousands of years.
How did scientists find prehistoric plague?
An international team of scientists sequenced genetic material from ancient teeth found at four hunter-gatherer cemeteries. They reconstructed bacterial genomes to identify previously unknown early strains of the disease.
The team detected DNA from Yersinia pestis in 18 of 46 individuals studied. Lead author Ruairidh Macleod, now a Research Fellow at the University of Oxford, stated that the combination of plague DNA, radiocarbon dating, and archaeological analysis provided a complete picture of these outbreaks.
Nearly 40 percent of the remains showed evidence of infection. Researchers noted that this detection rate is higher than some reported rates from medieval plague burial sites.
Why was early plague so deadly?
Previous research suggested early plague strains were mild because they lacked the genetic features needed to spread via fleas and rodents. This new evidence contradicts those beliefs.
Archaeologist Andrzej Weber of the University of Alberta found an unusually high number of children and young teenagers in the two largest cemeteries. Weber noted that this pattern had been a puzzle since the 1990s until plague was identified as the cause.
Radiocarbon dating showed many burials happened in a short window. Some parents and children, or siblings, died and were buried together.
The role of the superantigen
Researchers identified a distinctive superantigen in these ancient strains. This toxin-producing genetic factor is not found in later historic plague strains.

According to senior author Martin Sikora, an Associate Professor at the University of Copenhagen, superantigens trigger powerful immune reactions and severe inflammatory responses. This combination of virulence factors likely made the infections highly lethal, especially for children.
Where did the disease originate?
The study supports the theory that plague first emerged in North-East or Central Asia. It likely spread across Eurasia through wild rodent populations.
Archaeological evidence shows the hunter-gatherers had close contact with marmots. These large burrowing rodents still carry plague today, and researchers believe the disease passed directly from marmots to humans.
What may happen next?
Future research could explore other prehistoric sites in Central Asia to see if similar superantigens existed in other early populations. Scientists may also look for further genetic links between these ancient strains and the later bubonic plague.
Additional analysis of ancient remains could potentially reveal how the bacterium eventually transitioned from direct animal-to-human contact to the flea-borne transmission seen in later centuries.
Frequently Asked Questions
When did these prehistoric plague outbreaks occur?
The outbreaks occurred approximately 5,500 years ago.
Who was most affected by the early plague?
Researchers found an unusually large number of children and young teenagers among the dead in the largest cemeteries.
How did the plague spread to these prehistoric humans?
Researchers believe the disease may have passed directly from infected marmots, which are large burrowing rodents, to the hunter-gatherer populations.
Does this discovery change your perspective on how ancient diseases shaped human history?