The plague of the Black Death wiped out nearly half of Europe’s population in the 13th century. Now, a genetic analysis published in the journal Cell Reports reveals the discovery of Yersinia pestis , the bacteria that caused the deadly epidemic, in the remains of a 5,000-year-old hunter-gatherer. The results indicate that this strain was probably less contagious and virulent than its medieval version.
“The most surprising thing about this finding is that it takes us two thousand years ahead of the appearance of Y. pestis, ” explains Ben Krause-Kyora, lead author and director of the DNA laboratory at the University of Kiel in Germany. “It seems that we are very close to locating the origin of the bacteria.”
The plague-bearing hunter-gatherer was a 20 to 30-year-old man named RV 2039, and he was one of two people whose skeletons were discovered in an excavation in the late 19th century in present-day Latvia.
A surprising find
Krause-Kyora and her team used tooth and bone samples from the four hunter-gatherers to sequence their genomes and then analyzed them for bacterial and viral pathogens. They were surprised to find evidence of Y. pestis in RV 2039, and after reconstructing the genome of the bacterium and comparing it with other ancient strains, the researchers determined that the Y. pestis RV 2039 found was, in fact, the oldest strain ever discovered. It was likely 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 .
“In this very early strain we already see the genetic set of Y. pestis practically complete, and only a few genes are missing. But even this small difference in genetic makeup can have a huge influence on virulence, ”explains the researcher.
Why was the bubonic plague a deadly epidemic?
In particular, this ancient strain was missing something critical: the gene that allowed fleas to act as vectors to spread the pest. This gene was responsible for the efficient transmission of the bacteria to human hosts, resulting in the growth of the well-known pus-filled buboes in the sick associated with medieval plague. Flea-based transmission also required the death of the human host, meaning that the appearance of the gene could have propelled evolution into a more deadly disease.
As of RV 2039, it probably took Y. pestis over a thousand years to acquire all the mutations necessary for flea-based transmission. And it’s unclear to what extent RV 2039 experienced the effects of the plague. Y. pestis was found in his bloodstream, meaning that he most likely died from the bacterial infection, although the researchers believe that the course of the disease could have been quite slow.
They observed that he had a large number of bacteria in his bloodstream at the time of his death, and in previous studies with rodents, a high bacterial load of Y. pestis has been associated with less aggressive infections . Furthermore, the people he was buried near were not infected and RV 2039 was carefully placed in his grave, which, according to the authors, also makes a highly contagious respiratory version of the plague less likely.
If the early form of Y. pestis did indeed produce a slow-moving, low-contagious disease, the finding challenges many theories about the development of human civilization in Europe and Asia. For example, some historians have suggested that infectious diseases such as that caused by Y. pestis evolved primarily in megacities of more than 10,000 people near the Black Sea. However, 5,000 years ago, the age of the RV strain 2039, large cities did not yet exist: agriculture was beginning to appear in Central Europe and populations were much smaller. Furthermore, this new theory also contradicts the hypothesis that Y. pestis led to the great population decline in Western Europe at the end of the Neolithic Age.
The authors also consider that the Y. pestis story could shed light on human genomic history. “Different pathogens and the human genome have always evolved together. We know that Y. pestis probably killed half the European population in a short period of time, so it should have had a huge impact on the human genome,” he says. Krause-Kyora. “But even before that, we see a big change in the genes of our immune system at the end of the Neolithic, and it could be that we were also seeing a significant change in the pathogen landscape at that time .”
