A plague pandemic occurred in a small hunter-gatherer society in Siberia 5,500 years ago, researchers have found. The plague, known as the Black Death, had been thought to have begun as agriculture advanced and populations surged. The findings are being hailed as the earliest evidence of a Black Death pandemic.
An international team led by Eske Willerslev of the University of Copenhagen in Denmark said on the 18th in the journal Nature that it found DNA from the plague bacterium in the remains of hunter-gatherers excavated from four cemeteries around Lake Baikal in Siberia. Scientists from Britain, the United States, Canada, China and Russia also took part in the study.
◇ Plague bacteria in 40% of remains, evidence of a pandemic
Plague is an infectious disease caused by the bacterium Yersinia pestis, which is spread by rats and fleas. It was called the Black Death because patients' skin turned black. According to the World Health Organization (WHO), more than 50 million people died in the 14th-century Black Death in Europe. It spread mainly in densely populated cities.
The team extracted and analyzed bacterial DNA from the teeth of hunter-gatherer remains buried in Siberian cemeteries. They detected plague DNA in 18 of 45 individuals, or 40%. Based on this, they estimated that plague pandemics struck Siberia's hunter-gatherer societies twice, 5,520 to 5,265 years ago and 5,315 to 4,235 years ago.
Although fewer than half the skeletons yielded plague bacteria, the team called it a pandemic because of DNA characteristics. Even if a person died of plague, over time the pathogen's DNA in bone or teeth degrades and disappears. At London's East Smithfield cemetery, where 14th-century plague victims were buried, only 20% of remains yielded plague DNA. In this light, the discovery is considered strong evidence of an ancient plague pandemic.
Hunter-gatherer societies had lower population density than agrarian societies and were mostly small family groups. The team said the detection of plague bacteria in graves where family members or relatives were buried together indicates transmission through close contact in such small communities. Even amid the spread of plague, bodies were buried facing the direction of river flow in line with funerary customs, suggesting tightly bonded family groups, they added.
◇ Direct animal-to-human infection without fleas
The researchers said the Siberian outbreak, unlike the medieval period, was pneumonic plague transmitted through the respiratory tract. Medieval plague was bubonic plague spread by rat fleas. That means fleas that fed on plague-infected rats then bit humans, transmitting the bacteria to the lymph nodes. The lymph nodes would then swell to the size of an egg and cause severe pain (buboes).
Genetics also pointed to pneumonic plague. Unlike medieval strains, the ancient plague bacteria lacked the ymt gene. The protein encoded by this gene protects plague bacteria so they can proliferate in a flea's gut. Without ymt, the plague cannot spread via fleas. That suggests the bacteria jumped directly from animal hosts to humans.
Many marmot teeth and bones, from a rodent species, were found in and around the Siberian graves. The team inferred that the deceased hunted marmots and processed their meat in life. If so, body fluids or blood from plague-infected marmots could have entered human lungs as aerosols (fine particles). DNA of Brucella, a bacterium transmitted through animals, was also found in ancient remains. This suggests hunter-gatherers frequently encountered wild animals and were constantly exposed to disease risks.
Another feature of the ancient plague is that the victims were mainly children ages 8 to 11, before puberty. Martin Sikora of the University of Copenhagen, a co-corresponding author, said, "Even before evolving efficient flea-borne transmission, ancient plague strains appear to have carried a potent combination of virulence factors capable of making infections deadly."
The team said the ancient plague strains carried the YPM superantigen gene. Ordinary antigens trigger appropriate immune responses when matched with their corresponding antibodies, but superantigens bind indiscriminately and forcefully, provoking explosive immune reactions. Adults, having been exposed once in childhood and acquired immunity, may be less sensitive to superantigens, but children with weaker immunity would have been defenseless, the researchers explained.
References
Nature (2026), DOI: https://doi.org/10.1038/s41586-026-10540-5