The oldest known plague outbreak struck Siberian hunter gatherers 5,500 years ago

This horrid disease has been with us for much longer than we thought.

When most people think of plague, they picture medieval cities, packed streets, and the Black Death. However, new research suggests the disease’s history stretches much further back.

A new preprint study has uncovered evidence of deadly plague outbreaks among hunter-gatherers living near Lake Baikal in Siberia around 5,500 years ago. This makes it the oldest known plague outbreak ever identified.

Until now, many researchers believed that plague epidemics required dense populations, close human-animal contact, and lifestyle changes that emerged with agriculture during the Neolithic period. The new study provides direct evidence that plague was already causing deadly outbreaks long before farming and cities became widespread. 

Tracing a prehistoric outbreak

To investigate the origins of plague, researchers analyzed ancient DNA from 42 hunter-gatherers buried at four cemeteries around Lake Baikal. The team searched for traces of pathogens preserved in skeletal remains and found DNA from Yersinia pestis, the bacterium that causes plague.

Across the sampled sites, about 39% of individuals showed evidence of plague infection. At Ust’-Ida I, the largest cemetery in the study, the detection rate was 38.7%. The plague was really common, far more common than other pathogens found in the remains.

The team then combined ancient bacterial genomes, radiocarbon dating, and kinship analysis to reconstruct what may have happened. Their results point to two early phases of infection, beginning roughly 5,600 to 5,400 years before present.

The first outbreak appears to have unfolded within a single generation. That points to a fast-moving disease, not a random collection of isolated infections.

Children seem to have suffered the most

The family evidence is especially striking. Several infected people belonged to small kin groups. In some cases, close relatives carrying plague were buried in different graves, suggesting they did not all die in one single event. Instead, they may have been infected during separate waves of transmission.

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The cemetery evidence also suggests the infections were severe. These weren’t people living with the pathogen for a long time; researchers found signs of acute mortality, meaning people likely died soon after infection.

Children appear to have been especially vulnerable. The study authors note that plague infections at Cis-Baikal seem to have hit children particularly hard, with several severe cases found in children around 8 to 11 years old.

That pattern is consistent with person-to-person spread, although ancient DNA cannot prove the exact route of transmission.

What the ancient genomes revealed

The newly identified strains sit on a very early branch of the Y. pestis family tree. According to the researchers, they diverge before all previously known Y. pestis diversity and push back the split between Y. pestis and its close relative Y. pseudotuberculosis by about 2,000 years. In other words, these genomes capture plague close to the beginning of its evolutionary history.

“Our phylogenetic analysis reveals that these virulent plague strains are temporally relatively close to the most recent common ancestor of Y. pestis and Y. pseudotuberculosis,” the study authors said.

The outbreaks may have started when the bacterium jumped from wild animals into humans. The authors suggest wild marmots around Lake Baikal as a likely source. Marmots are known plague reservoirs today, and they would have been familiar animals to hunter-gatherers in the region.

Once plague entered these communities, it may have spread between people. That would make these outbreaks very different from the classic image of bubonic plague, which depends heavily on flea transmission.

Later plague strains acquired genetic features that helped the bacterium survive in fleas and spread more efficiently through flea bites. One important gene, called ymt, plays a major role in flea-mediated transmission. The strain that researchers found lacks this gene, suggesting the plague wasn’t yet spreading through fleas.

So the Lake Baikal plague may have spread through close contact, perhaps through respiratory droplets. But that remains an inference, not a confirmed diagnosis of pneumonic plague.

Why this changes plague history

The findings challenge the idea that deadly plague outbreaks required farming societies, large populations, or animal domestication. Instead, they show that severe epidemics could strike small, mobile hunter-gatherer communities thousands of years before the rise of agriculture. 

The study also supports a central or northeastern Asian origin for plague and provides a rare glimpse into the pathogen’s earliest evolution.

However, important questions remain. Ancient DNA can reveal which pathogens infected people, but it cannot fully reconstruct symptoms or transmission routes. The researchers hope to analyze additional ancient samples to better understand how early plague spread across Eurasia.

“Together, our findings underscore the universality of zoonotic infection, given the markedly different lifeways of prehistoric hunter-gatherers from European Neolithic farmers,” the study authors said.

With about 75 percent of emerging human diseases originating in animals, the researchers say understanding ancient spillover events could help shed light on the emergence of infectious diseases today.

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The study is published in the journal Nature.