Plague is commonly associated with rats, congested medieval cities, and the catastrophic epidemics that ravaged Europe during and after the Middle Ages.
However, new research published in Nature reveals that the disease was already a lethal threat some 5,500 years ago. During that period, it was wiping out members of small, nomadic hunter-gatherer communities — long before the advent of agriculture and urbanization created the dense living conditions typically linked to major plague outbreaks.
Ancient DNA Uncovers Early Plague
An international research team analyzed ancient DNA extracted from human remains at four hunter-gatherer burial sites in the Lake Baikal region of East Siberia. By sequencing genetic material preserved within teeth, the scientists reconstructed ancient bacterial genomes and identified previously unknown early variants of plague.
“Whether the earliest forms of plague were mild or highly virulent has been a subject of debate, but our findings demonstrate that these ancient strains were already extremely lethal,” says senior author Eske Willerslev, Professor at the University of Copenhagen and the University of Cambridge.
To piece together what transpired within these prehistoric communities, the researchers integrated genetic evidence with archaeological findings and radiocarbon dating.
“Through the plague DNA, the genetic relationships among the victims, the archaeological analysis, and the radiocarbon dating, we have constructed a remarkably clear and complete picture of what occurred during these outbreaks,” says lead author Ruairidh Macleod, who conducted the research as a PhD student at the University of Cambridge and is now a Research Fellow at the University of Oxford.
The team identified DNA from Yersinia pestis — the bacterium responsible for plague — in 18 of the 46 individuals tested. This means that nearly 40 percent of the sampled individuals carried evidence of plague, a detection rate even higher than those reported at certain medieval plague burial sites.
Early Plague May Have Been Far More Deadly Than Previously Thought
Prior research had demonstrated that ancient strains of Yersinia pestis lacked certain genetic features that eventually enabled bubonic plague to spread efficiently via fleas and rodent hosts. For this reason, scientists had generally assumed that the earliest versions of the bacterium were unlikely to trigger severe epidemics.
The new findings challenge this assumption.
At the two largest cemeteries, researchers discovered an strikingly high number of children and young teenagers among the deceased. Archaeologists had struggled for decades to explain why so many young individuals were interred there over such a brief period.
“The unusually large number of children and the short timespan were a real puzzle we have been trying to solve since the 1990s. Learning that plague was the cause is remarkable, but it also makes perfect sense,” says archaeologist Andrzej Weber of the University of Alberta, Principal Investigator of the Baikal Archaeology Project.
Radiocarbon dating indicates that many of the deaths occurred in close temporal proximity. In some cases, siblings appear to have perished together, while other graves contain parents and children who likely died during the same outbreak.
A Possible Clue to the Plague’s Deadliness
The ancient plague strains also possessed a distinctive superantigen — a toxin-producing genetic element not observed in later historic plague strains. Superantigens can provoke an exaggerated immune response, potentially causing severe inflammation and rendering an infection far more dangerous.
“This finding reshapes our understanding of the earliest plague outbreaks: even before the bacterium evolved efficient flea-borne transmission, these ancient strains appear to have carried a powerful combination of virulence factors capable of making infection highly lethal,” says senior author Martin Sikora, Associate Professor at the University of Copenhagen.
Taken together, the evidence suggests that some of the earliest known plague outbreaks were already as deadly as later historical epidemics, particularly among children. This appears to have been possible even before the bacterium developed the efficient flea-based transmission associated with later bubonic plague.
Did Plague Spread from Marmots to Humans?
The findings also bolster the theory that plague may have first emerged in Central or Northeast Asia before spreading more broadly across Eurasia through populations of wild rodents.
Archaeological evidence indicates that the hunter-gatherers inhabiting the Lake Baikal region had close contact with marmots — large burrowing rodents that still carry plague today. Researchers therefore suspect that some of these prehistoric outbreaks may have originated when the disease was transmitted directly from infected marmots to humans.
If so, plague was already capable of causing deadly outbreaks in small human communities thousands of years before the emergence of cities, dense settlements, and the flea-driven epidemics that would later make the disease notorious.
