Earliest Strain of Plague Found in 5,000-year-old Latvian Man, and It Was Mild

The plague bacteria found in the hunter-gatherer who died at a riverside village in ancient Latvia didn’t even have the gene to enable infection by flea

Ruth Schuster
Ruth Schuster
Cranium of 5,000-year-old Latvian who had earliest known strain of Yersinia pestis
Cranium of 5,000-year-old Latvian who had earliest known strain of Yersinia pestis (propped up by a vial)Credit: Dominik Gldner, BGAEU, Berlin
Ruth Schuster
Ruth Schuster

A man buried more than 5,000 years ago in Latvia had the plague, archaeologists announced on Tuesday. Though the disease caused by the bacteria Yersinia pestis as we know it today is highly dangerous, it may not have been what killed him. The aged among us who lived through pandemics in the last century could rightly grouse: Plague isn’t like it used to be. The disease it causes had been milder at its inception, it seems.

Genetic analysis of the bacteria extracted from the remains of the plague-ridden hunter-gatherer, published in the journal Cell Reports, indicates that the ancient strain was likely less contagious and not as deadly as the medieval version behind the disease known as the “Black Plague.”

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Yersinia pestis, cause of the plague, is believed to be a mutation of Yersinia pseudotuberculosis that split from its bacterial family about some 7,000 years ago, write Julian Susat of Kiel University, Germany and colleagues in Cell Reports. The genome of the germ that infected this unfortunate hunter-gatherer whose remains were found at the prehistoric riverside settlement of Rinnukalns, Latvia was reconstructed, shoring up the thesis that the basal lineage of the “plague bacteria” had indeed begun in the early Neolithic revolution (which was later in Europe than in Israel, the Levant and the Middle East).

The hunter-fisher-gatherer was in one of two graves found in 1875 in association with a shell midden – mussel shells and fish bones dating to the early 6th millennium B.C.E. One of the graves contained the remains of a young teenage girl and the other contained the remains of a young man, aged 20 to 30.

As we all know, during the 20th century there were two world wars, things get misplaced and one can lose track of things. Long story short, the bodies were lost – they “seem to have disappeared,” as the archaeologists put it. And then lo, in 2011 their skulls were rediscovered in a box at the Berlin Society of Anthropology; also, in the meanwhile archaeologists excavating the prehistoric settlement found two more graves, one of a newborn.

The archaeologists hadn’t been looking for the earliest known plague victim, or Yersinia pestis sufferer. They had wanted to look at the genomic composition of these hunter-gatherers because not much is known about the population of Latvia some 5,000-plus years ago.

“Surprisingly, in one male, we identified the genome of Yersinia pestis, the infectious agent responsible for at least three historical plague epidemics,” the authors write.

Mass death, or not

Let us interject here that there is some fog over historic pandemics. For instance, what may have been bubonic plague but could have been some other pestilence is mentioned in early sources, such as a disease called the “Hittite plague” ravaging the Levant and Middle East (including Megiddo) in 1,350 B.C.E., or the disease in Athens in 429 B.C.E. There are plenty of examples but we tend to look mainly at three supposed episodes in more familiar history, starting with the "Justinian plague" of the 6th century C.E., and the medieval plague.

However, some researchers such as Hebrew University's Lee Mordechai and colleagues have observed the absence of concrete proof of mass graves in the 6th century and in the places associated with the Justinian plague and surmise that the disease was hyped by local scribes: It may have been localized but was later assumed to have been continent-wide. On the other hand separate research found that in the medieval U.K., plague victims weren’t all tossed into mass graves; at least some were interred in individual graves “with compassion.”

So who knows. But going back to our Latvian hunter-gatherer-fisher with Yersinia 5,300 to 5,050 years ago: In the process of looking to find his antecedents, what scientists found in the pathogen screen was an early plague bug.

How do they know this bug was weaker, by which we mean, likely less infectious than the pathogen that caused the Black Death et al? Because it was missing a certain genetic virulence gene called ymt, which has also been found in some other ancient pestis strains, though this one is the oldest so far. It did have other virulence genes though.

The researchers even conclude that this Rinnukalns strain was a scion of the first branching event of the plague strain off the Y. pseudotuberculosis tree, and evolved off into a clade of its own, distinct from later branches that produced later Neolithic and Bronze Age strains.

Their estimates of the divergence were based on molecular clock analyses. Thusly they estimate that this man’s Y. pestis originated from bacteria that split from Y. pseudotuberculosis 7,400 years ago, at most a few centuries before he lived.

“What’s most astonishing is that we can push back the appearance of Y. pestis 2,000 years further than previously published studies suggested,” says senior author Ben Krause-Kyora, head of the DNA Laboratory at the University of Kiel in Germany. “It seems that we are really close to the origin of the bacteria.”

Blame not the rat

Crucially, another thing lacking in this ancient strain of plague was the gene that enables fleas on rats to act as vectors to spread the plague, which is widely believed to be how people were originally and are exposed to plague.

“This gene was responsible for efficient transmission of the bacterium to human hosts, which resulted in the growth of the infamously grotesque pus-filled buboes in the sick associated with the medieval bubonic plague,” the authors explain.

A rat: Not guilty! The earliest strain of Yersinia pestis didn't have the gene for transmission by rat fleasCredit: Reinhold, Sanguinetti-Scheck, Hartmann & Brech/AFP

So how did he get it? Maybe through a cut that got infected or bite from an infected animal. The bacteria had been in his bloodstream, the authors write, so he may have died of sepsis – but possibly not of plague per se.

Also, not that the sample is large, but his was the only body found to have pestis. That too indicates that he hadn’t developed the contagious respiratory version of the plague. He may not have had “plague” at all.

Later versions of pestis would be flea-transmissable and deadlier.

Meanwhile, one theory this theory debunks is that plague first arose in the early megacities (at the time, meaning more than 10,000 people) around the Black Sea. But this man died before these cities arose; agriculture and its accompanying rodent companions may have begun thousands of years before in the Levant, but not in Europe or Latvia; ergo Yersinia pestis was not a bastard child of the filthy first megacities, and it also likely had nothing to do with the apparent population collapse in Western Europe during the late Neolithic Age, 5,000 to 6,000 years ago, even though some have blamed that on the bacteria (based for instance on finding evidence of the early germ in Neolithic farmers in Sweden) . We still don’t know why that happened.



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