Oldest-known plague outbreak came 5,500 years ago in Siberia

About 5,500 years ago, bands of hunter-gatherers inhabited the Lake Baikal region in Siberia, sustained by rich resources including prey such as elk, deer, moose, fish, seals and rodents called marmots. These ​people became victims of the earliest-known plague outbreak, especially children and adolescents.

Researchers said ancient DNA obtained from bodies interred in four burial sites in the area revealed the ‌presence of the oldest-known strains of Yersinia pestis, the plague bacterium. These prehistoric deaths presaged the immense suffering that this pathogen has visited on humankind over the millennia.

The researchers said the outbreak was particularly deadly for the young, judging from the burial sites, and attributed this to genetic traits in these strains that no longer are present in today’s iteration of the pathogen. They also said the discovery adds to evidence that marmots were the bacterium’s original ​host species, and that plague arose in central or northeastern Asia before spreading across Eurasia.

“The findings fundamentally change how we think about the origins and early impact of one ​of humanity’s most consequential pathogens,” said evolutionary geneticist Eske Willerslev of the University of Copenhagen and the University of Cambridge, senior author of the study ⁠published on Wednesday in the journal Nature.

The next oldest-known instance of plague dates to between 5,300 and 5,000 years ago in Latvia, roughly 3,000 miles (5,000 km) away.

“It’s only with the development of methods ​for studying ancient DNA that we’ve discovered it’s been around a lot longer than what we know from historical records. It’s a zoonotic disease, a pathogen maintained primarily in rodents rather than humans, but ​which has repeatedly spilled over into humans with devastating effects,” University of Oxford evolutionary geneticist and study lead author Ruairidh Macleod said.

These effects included two epidemics that killed a large percentage of Europe’s population – the 6th-century Plague of Justinian and 14th-century Black Death, when plague was transmitted to people through bites by infected fleas carried by rats.

It long had been supposed that significant plague outbreaks occurred only after humankind began agriculture and established settlements with high ​population densities. There also were thoughts that early strains may have been mild. The discovery that plague killed prehistoric hunter-gatherers roaming a remote forested landscape in bands numbering perhaps in the dozens contradicted ​those notions.

At Lake Baikal, Yersinia pestis was detected in 18 of 46 bodies examined, a higher rate than in some medieval plague burial pits. Macleod said finding evidence of a large-scale lethal plague outbreak among these ‌hunter-gatherers was a “complete ⁠surprise.”

‘A TRANSITIONAL STAGE’

The researchers recovered multiple Yersinia pestis genomes preserved in the teeth of buried plague victims. These strains were very close to the ancestral root of a bacterium that had diverged from its evolutionary predecessor perhaps only two centuries earlier.

“The pathogen appears to represent a transitional stage in plague evolution – already capable of causing severe disease but not yet possessing the full suite of adaptations seen in later pandemic strains,” Willerslev said.

The ancient strains lacked a gene required for efficient flea-borne transmission and for painful swellings triggered by the infection spreading from flea bite sites to the nearest lymph nodes, ​as occurred in the later epidemics.

But they possessed ​a genetic variant absent in later plague ⁠strains that can cause severe inflammatory complications to which children are especially susceptible. Many of those buried were children, sometimes siblings.

“This susceptibility is highest for 8-to-12-year-olds, and is clearly a completely different pattern of mortality to what we see at other Baikal hunter-gatherer sites where plague is not detected,” Macleod ​said.

“Combined with the presence of other genes that make plague infections severe, it is clear that these prehistoric plague strains were just as capable ​of being deadly, if ⁠in a different way,” Macleod said.

These hunter-gatherers came into close contact with marmots, and the researchers said it appears the rodents fueled the outbreak. At other sites, pendants made with the front teeth of marmots were included in burials. Marmots also would have been a source of food.

“Some people might have come in contact with an infected marmot, likely handling one, or eating undercooked marmot meat,” Macleod said.

After the pathogen had ⁠jumped from marmots ​to people, the researchers believe it spread via human-to-human transmission, for example by coughing.

“The plague infections are widespread between ​individuals, with many closely related individuals apparently having died of plague at the same time,” Macleod said.

“This outbreak devastated hunter-gatherer communities at the time. It’s clear that at least a few people were left alive to bury the dead, and they ​clearly knew who was who, with young siblings buried together in shared graves,” Macleod said.