The Plague of Justinian, the Black Death, and the Third Plague: The death and terror caused by Yersinia pestis have marked human history for millennia.
One prevailing theory is that the emergence of this infectious disease was driven by the development of agriculture, a sort of Faustian bargain in which a predictable food supply attracted pests that carried the deadly bacterium. Archaeologists speculate that hunter-gatherers moved around too much and lived in too small of groups for Y pestis to cause much harm.
Research published today turns that theory on its head. A study in the journal Nature shows that hunter-gatherers in Siberia were dying of the plague approximately 5,500 years ago, making it by far the earliest known outbreak in the archeological record, said lead author Ruairidh Macleod, PhD, a postdoctoral research fellow at All Souls College, University of Oxford.
For comparison, the Justinian Plague, which is often called the first known pandemic, occurred around the year 540. The Black Death originated in Central Asia in the early 1330s, with the Third Plague pandemic starting in China around 1855.
"The fact that we're finding this happening in an isolated group of prehistoric hunter-gatherers is really, really extraordinary to me and challenges a lot of that epidemiological theory," said Macleod, who noted these groups had no contact with any people participating in any sort of agricultural or pastoral activity.
Mysterious deaths of children finally solved
Lake Baikal is a resource-rich region in southeast Siberia where archaeologists have documented at least 65 cemeteries from the late Mesolithic to the early Bronze Age. The earliest dates back more than 8,000 years.
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Credit: Vladimiri Bazaliiskii / Baikal Archaeology Project
One of the larger burial sites has confounded researchers since the 1990s because of the disproportionate number of graves belonging to children and adolescents. Skeletal remains at Ust’-Ida show these young people did not suffer violent deaths, and radiocarbon evidence indicates they died within a very short period.
Recent DNA sampling of teeth found that at least 18 of the 46 children and adolescents buried at Ust’-Ida and several other cemeteries likely died of plague.
These specimens come from skeletons that were excavated by the Baikal Archaeology Project, an international team of researchers headquartered at the University of Alberta in Canada. Macleod drilled into the tip of each molar or premolar, taking somewhere between 50 and 100 milligrams of material that was then crushed into a powder to extract DNA.
Blood vessels in the center of the tooth can leave behind DNA, though this genetic material doesn't preserve well. Macleod said the fact that 39% of the graves were positive for Y pestis is remarkable, and he suspects most, if not all, 46 children and teens perished from the disease.
For context, just 20% of bone and tooth specimens taken from the East Smithfield plague pit in London that were tested were positive for Y pestis. This emergency burial ground was created in the mid-14th century during the Black Death, which claimed the lives of 30% to 50% of Londoners.
Two plague outbreaks, 300 years apart
The earlier plague outbreak near Lake Baikal occurred between 5,520 and 5,265 years ago. It involved individuals at Ust’-Ida, along with those interred at the smaller site of Shumilkha. Both cemeteries sit on the banks of the Angara River, a major watercourse draining from the lake.
These burial grounds are about 23 miles apart, and DNA testing revealed that each cemetery belonged to a specific band or family. However, radiocarbon dating and genomic analysis across both sites produced very similar results, which is why Macleod and his colleagues believe that young people buried at either cemetery died from the same outbreak.
Credit: Jacques Descloitres, NASA
"It's very likely that they could have come in contact with each other, as they're constantly moving around the landscape," he explained.
The researchers also examined specimens from Bratskii Kamen and Serovo, two other cemeteries farther up the Angara that belong to other family groups. Radiocarbon dating was more variable at these locations. However, the number of specimens detected with Y pestis led the researchers to believe that at least some of the children and teenagers buried at these locations died during a second outbreak of plague that occurred some 300 years after the first.
For example, one grave at Bratskii Kamen was shared by three girls, likely two sisters and their first cousin. (The trio inherited the same rare mutations from the maternal line, indicating their mothers were possibly sisters.) The girls were between the ages of 4 and 9 years, and each had Y pestis when she died.
The reason children were dying, but their parents were not, is that the prehistoric strains carried a superantigenic toxin that is not present in more recent waves of the plague. This superantigen triggered an extreme immune response that was possibly similar to Kawasaki syndrome, which is more common among young children.
"We have lots of cases of, unfortunately, siblings having died at the same time and buried at the same time in shared graves," said Macleod.
Outbreaks likely started with marmots
Marmots were one of the animals that Siberian hunter-gatherers consumed. These large ground squirrels are a reservoir of Y pestis, which continues to pose a risk to human health. Macleod and his collaborators suspect that zoonotic spillover from marmots started both outbreaks, which then spread person-to-person.
Credit: Kelvin Wilson
These findings also conclusively dispel another theory that prehistoric strains of the plague were less lethal than those that circulated during antiquity and the Middle Ages. The number of children buried near Lake Baikal shows that Y pestis was highly virulent, contagious and devastating.
The idea that the lifestyle of hunter-gatherers somehow protected them from plague never fully made sense, said Macleod, given that infectious diseases wreak havoc on animal populations. For example, in the 1990s, Ebola virus disease contributed to declines in the number of wild gorillas and chimpanzees living in Gabon and the Republic of Congo.
Also, some Neanderthal genomes have strong selection for immune variants associated with RNA viruses. And there's evidence suggesting that Neanderthals were infected by diseases brought to Europe by Homo sapiens, who migrated from Africa.
The threat of infectious disease is universal for humans, said Macleod. There was never a time we were safe from pathogens.
