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The skull of the man who died infected with an early strain of the bacterium that thousands of years later caused the devastating plague in medieval Europe. Black Death origins have now been pushed much further back in history because of this incredible scientific study.					Source: Dominik Göldner / BGAEU

Black Death Origins Linked To 5,000-year-old Latvian Man

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The remains of an ancient hunter-gatherer unearthed long ago at the Rinnukalns archaeological site in Latvia, has tested positive for Yersina pestis, which is better known as the bacteria behind the Black Death plague of the Middle Ages in Europe. The individual, referred to as RV 2039, was dated to 5,000 years ago. This is the earliest evidence of the Black Death plague strain that would eventually kill 30-60% of the European population in the middle of the 14th century. This means Black Death origins unfolded much earlier than previously believed.

This historical breakthrough was the outcome of genetic analysis and research study published in the journal Cell Reports . “Surprisingly, in one male, we identified the genome of Yersinia pestis, the infectious agent responsible for at least three historical plague epidemics,” the authors wrote.

(A) Map showing the Rinnukalns site where the individuals presented in this study were recovered. (B and C) Cranium (B) and mandible (C) of individual RV 2039 rediscovered in the Rudolf Virchow Collection at the Berlin Society of Anthropology, Ethnology and Prehistory (BGAEU).

(A) Map showing the Rinnukalns site where the individuals presented in this study were recovered. (B and C) Cranium (B) and mandible (C) of individual RV 2039 rediscovered in the Rudolf Virchow Collection at the Berlin Society of Anthropology, Ethnology and Prehistory ( BGAEU).

Black Death Origins: Pushing Back History With Science

In the study, ancient DNA (aDNA) analysis and pathogen screening was performed on the 4 individuals found at the Rinnukalns site. One of the individuals, a specimen named RV 2039, was a 20-30-year-old man, who showed traces of the Y. pestis plague strain , though it probably didn’t cause his death.

The researchers reconstructed the bacterium's genome and compared it to 41 ancient and modern Y. pestis strains. They found that a strain branching event had occurred some 7,000 years ago. This resulted in a split from the Yersinia pseudotuberculosis (which causes Far East scarlet-like fever). From this point in time, the new strain evolved into a distinct clade (organism group), which was similar but also different from later forms that produced the deadly Black Death strains.

The previously oldest known date of the Y. pestis strain was discovered in a Swedish peasant farmer from 5,000 years ago. She was 20 years old, and the cause of her death was the very same bacteria. "It seems this bacterium has been around for quite a long time. What's most astonishing is that we can push back the appearance of Y. pestis 2,000 years farther than previously published studies suggested. It seems that we are really close to the origin of the bacteria," said senior author Ben Krause-Kyora, head of the aDNA Laboratory at the University of Kiel in Germany, and co-author on the latest Black Death origins study.

The RV-2039 individual had a fascinating history. He was one of two skeletons excavated in 1875 at a burial site in present-day Latvia. The burial was connected with an ancient shell midden dated to the early 6th millennium BC, as reported in Haaretz. The remains unearthed in both graves were lost, during the chaos of the first and second world wars. Luckily, in 2011, their skulls were rediscovered in a box, part of German anthropologist Rudolph Virchow’s collection, at the Berlin Society for Anthropology, Ethnology, and Prehistory.

After bone and teeth sampling, genome sequencing and reconstruction, and pathogen screening for both viral and bacterial pathogens, the research team’s biggest challenge was to determine why this ancient strain was not as potent as its medieval successor.

"What's so surprising is that we see already in this early strain more or less the complete genetic set of Y. pestis , and only a few genes are lacking. But even a small shift in genetic settings can have a dramatic influence on virulence," stated Krause-Kyora.

The deadly Black Death plague of the 14th century AD evolved in such a way that fleas became the transmission mechanism, and this caused the death tolls to rise at an incredible rate. (Aksana / Adobe Stock)

The deadly Black Death plague of the 14th century AD evolved in such a way that fleas became the transmission mechanism, and this caused the death tolls to rise at an incredible rate. ( Aksana / Adobe Stock)

Why Did the Early Black Death Bacteria Spread So Slowly?

In Epidemics and Society: From the Black Death to the Present (2019), by Frank M. Snowden, this question was answered rather well, and the answer is fleas. While the rats were the ones who provided the distribution method, it was actually the fleas on the rats who helped spread the bubonic plague. Fleas are also responsible for causing pneumonic plague , a variant of Y. pestis.

“It is known, however, that there are various strains of Y. pestis and that the strain responsible for the modern pandemic was overwhelmingly dependent on rats and fleas for its transmission. Rarely was it propagated by droplets or person-to-person transmission in the manner of the more virulent pneumonic plague that was so prominent,” Snowden noted. Essentially if rats had been the primary vector, the spread could never have been this quick.

The study confirmed the same: the ancient strain lacked the gene that let fleas act as vectors to spread the plague. Flea-based transmission also resulted in the death of the human host. RV-2039’s strain was at least a 1,000 years away from acquiring the genetic makeup and mutation required for Y. pestis to become a flea-based transmission mechanism.

The researchers of the latest Black Death origins study have suggested that RV-2039 was likely bitten by a rodent, like this wood mouse, carrying the earlier and milder form of the plague bacterium. (creativenature.nl / Adobe Stock)

The researchers of the latest Black Death origins study have suggested that RV-2039 was likely bitten by a rodent, like this wood mouse, carrying the earlier and milder form of the plague bacterium. ( creativenature.nl / Adobe Stock)

The researchers assume that the variant of the strain that RV-2039 had was mild and not too contagious. It did not spread to any other graves or skeletal remains, suggesting that despite a high bacterial load, the disease was not virulent enough to cause death. Since flea-based mutation was yet to occur, he was probably bitten by a rodent carrying the bacterium.

"Isolated cases of transmission from animals to people could explain the different social environments where these ancient diseased humans are discovered. We see it in societies that are herders in the steppe, hunter-gatherers who are fishing, and in farmer communities--totally different social settings but always spontaneous occurrence of Y. pestis cases," said Krause-Kyora.

Earlier studies had pointed to Y. pestis being the cause of massive population declines in Western Europe, that heralded the end of the Late Neolithic Age . The latest study clearly shows that the contagion was mild, if not limited, to human beings who had been bitten by infected rodents. In any case, 5,000-7,000 years ago the first urban settlements were yet to emerge, making rapid transmission impossible.

"Different pathogens and the human genome have always evolved together. We know Y. pestis most likely killed half of the European population in a short time frame, so it should have a big impact on the human genome. But even before that, we see major turnover in our immune genes at the end of the Neolithic Age, and it could be that we were seeing a significant change in the pathogen landscape at that time as well,” concludes Krause-Kyora.

Top image: The skull of the man who died infected with an early strain of the bacterium that thousands of years later caused the devastating plague in medieval Europe. Black Death origins have now been pushed much further back in history because of this incredible scientific study.                                                         Source: Dominik Göldner / BGAEU

By Rudra Bhushan

References

Conroy, G. 2021. Discovery of Black Death bacterium in 5,000-year-old body shows ancient roots of medieval plague . Available at: https://www.abc.net.au/news/science/2021-06-30/five-thousand-year-old-man-oldest-plague-strain/100249528.

Susat, J., Krause-Kyora, B., et al. 2021. A 5,000-year-old hunter-gatherer already plagued by Yersinia pestis . Cell Reports 35(13). Available at: https://doi.org/10.1016/j.celrep.2021.109278.

Schuster R. 2021. Earliest Strain of Plague Found in 5,000-year-old Latvian Man, and It Was Mild . Available at: https://www.haaretz.com/archaeology/earliest-strain-of-plague-found-in-5-000-year-old-body-in-latvia-1.9952043.

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