Prehistoric plague killed hunter gatherers 5,500 years ago

Plague is commonly associated with rats, crowded medieval cities, and the epidemics that swept across Europe during and after the Middle Ages.

But a new study published in Nature shows that the disease was already lethal 5,500 years ago, where it killed humans in small, mobile hunter-gatherer communities – long before the rise of agriculture and cities created the conditions usually associated with plague epidemics.

An international group of researchers analysed ancient DNA from human remains found at four hunter-gatherer cemeteries in the Lake Baikal region of East Siberia. Using advanced DNA sequencing techniques, the researchers reconstructed ancient bacterial genomes preserved in teeth, revealing previously unknown early strains of plague.

Whether the earliest forms of plague were mild or virulent has been a matter of debate, but our findings demonstrate that these ancient strains were already highly lethal."

Eske Willerslev, Senior Author, Professor, University of Copenhagen and the University of Cambridge

The study combines genetic, archaeological and radiocarbon evidence to reconstruct how the outbreaks unfolded within the prehistoric groups.

"Based on the plague DNA, the genetic relationships between the victims, the archaeological analysis and the radiocarbon dating, we've built a really clear, complete picture of what happened during these outbreaks," says lead author Ruairidh Macleod, who carried out the work while a PhD student at the University of Cambridge – and is now Research Fellow at the University of Oxford.

In total, DNA from Yersinia pestis – the bacterium that causes plague – was detected in 18 of 46 individuals – nearly 40 percent. This is higher than the detection rate reported from some medieval plague pits.

More lethal than previously thought

Previous studies showed that early strains of Yersinia pestis lacked some of the genetic traits that later enabled bubonic plague to spread efficiently via fleas and rodent hosts. This led many researchers to believe that the earliest forms of plague were unlikely to have caused major outbreaks.

However, the new study challenges that assumption.

The mortality profiles at the two largest cemeteries show an exceptionally high number of children and young teenagers among the dead – something that had puzzled archaeologists working on the graves for decades.

"The unusually high number of children and the short timespan was a real puzzle that we've been trying to solve since the 1990s. Finding out that plague was the cause is extraordinary, but it makes so much sense," says archaeologist Andrzej Weber of the University of Alberta, Principal Investigator of the Baikal Archaeology Project.

Radiocarbon dating showed that many of the burials occurred within a very short time span. In several cases, siblings or parents and children appear to have died and been buried together.

Did superantigen cause lethality?

The ancient plague strains also carried a unique superantigen – a toxin-producing genetic factor not seen in historic plague strains. Superantigens can trigger extreme immune responses and are associated with severe inflammatory complications, likely increasing the severity of infection.

"This finding changes our understanding of the earliest plague outbreaks: Even before the bacterium evolved efficient flea-borne transmission, these ancient strains appear to have carried a potent combination of virulence factors that could make infection highly lethal," says senior author Martin Sikora, Associate Professor at the University of Copenhagen.

Together, the findings suggest that the earliest known plague outbreaks may already have been as deadly as later historical forms of the disease, especially for children, even without flea-borne transmission.

The study also supports the idea that plague may have originated in Central or North-East Asia before later spreading across Eurasia through wild rodent reservoirs. Archaeological evidence suggests these hunter-gatherers interacted closely with marmots – large burrowing rodents that still carry plague today – and researchers believe the outbreaks may have spread directly from infected marmots into humans.