The oldest known strain of Yersinia pestis — the notorious bacteria behind the plague that caused the Black Death — has been discovered in the remains of a hunter-gatherer who died over 5,000-years-ago.
This new discovery, reported in the journal Cell Reports this week, pushes back the earliest discovery of Y. pestis by well over 1,000 years and suggests the bacteria strain was likely part of a lineage that emerged about 7,000 years ago, over 2,000 years earlier than other studies have previously found.
"What's most astonishing is that we can push back the appearance of Y. pestis 2,000 years farther than previously published studies suggested," Ben Krause-Kyora, senior study author and head of the aDNA Laboratory at the University of Kiel in Germany, said in a statement. "It seems that we are really close to the origin of the bacteria."
Evidence of the bacteria was discovered in the skeletal remains of a male in his 20s or 30s, dubbed “RV 2039,” who was buried over 5,000 years ago in a region known as Riņņukalns in present-day Latvia. The bones of this man were first discovered in the late 19th century alongside another skeleton. No one knows where the remains went for over a century until 2011 when they reappeared as part of German anthropologist Rudolph Virchow's collection. This rediscovery prompted researchers to return to the site, where they uncovered two more burials.
In the new research, a team of European scientists led by Kiel University in Germany studied samples from the teeth and bone of all four hunter-gatherers to sequence their genomes, as well as test them for an array of bacterial and viral pathogens. Much to their surprise, they found evidence of Y. pestis in RV 2039. Sequencing of the bacteria revealed its backstory and hints it was part of a lineage that emerged about 7,000 years ago, just a few hundred years after Y. pestis split from its predecessor, Yersinia pseudotuberculosis.
It’s unclear how the disease affected the victim, but it’s apparent he had a high bacterial load in his bloodstream at the time of death, suggesting he died from the infection. Importantly, it appears that his ancient strain was less contagious and not as deadly as the medieval descendent that infamously wiped out hundreds of millions of people in Eurasia and North Africa in the 14th century.
Genetic analysis of the bacteria shows it was yet to evolve a gene that allows flea-based transmission, a key factor that later helped the disease to spread like wildfire in the medieval period. As such, it appears this man was the sole victim of the disease after being bitten by an infected rodent. This likely caused a slow and ultimately deadly infection that was not transmitted to anyone else.
The discovery of the 5,000-year-old Y. pestis is set to rewrite the history of this notorious disease. Historians have assumed that plague and many other infamous infectious diseases first evolved in humans when the first ancient cities started to pop up around the Black Sea. With a densely packed population and increasing reliance on domesticated animal agriculture, urban centers would have provided the ideal melting pot for zoonotic diseases to jump from animals to humans. However, contrary to this idea, the new evidence comes from a hunter-gatherer who likely lived in a sparse population at a time when agriculture was only just starting to settle in Central Europe.
Given that early strains of Y. pestis appear to be significantly less transmissible and deadly than the later medieval strains, it could also dispel the idea that the plague brought significant population declines to Western Europe at the end of the Neolithic Age.
"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," explained Krause-Kyora.