Earliest known bubonic plague strain found in 5000-year-old skull

The bacterium behind the Black Death, which wrought devastation in medieval times, has been found in the skull of a man who lived 5000 years ago in what is now Latvia, making it the earliest known plague strain.

Analysis of ancient DNA in the hunter-gatherer’s skull suggests that the strain of Yersinia pestis, which causes the bubonic plague, was less transmissible and harmful than later versions, say Ben Krause-Kyora at Kiel University, Germany, and his colleagues. The lack of the bacteria in three other people buried next to the man, dubbed RV 2039, is one hint of a less deadly disease, says Krause-Kyora.

The apparent lower virulence leads the team to suggest that the plague wasn’t to blame for the decline of European people between 5000 and 6000 years ago, as claimed by a 2018 paper looking at Swedish farmers’ genomes.

“There’s an ongoing discussion as whether Y. pestis played a big role in the Neolithic decline,” says Krause-Kyora. “Our hypothesis is really contradicting the one before. It was maybe a more chronic, more omnipresent infection. It caused, for sure, some deaths, but it’s maybe not as severe as it became in the Middle Ages.”

Nonetheless, the high abundance of the bacteria found in the skull of the man, who was probably aged between 20 and 30 when he died, implies he succumbed to the plague, says Krause-Kyora. The man may have been bitten by a rodent such as a beaver, which are known to carry Y. pestis.  Remains of the animals have been found at the same site by the river Salaca in Latvia.

The evidence points to the plague spreading from animal to human at the time, rather than human to human, says Krause-Kyora. The bacteria hadn’t yet gained the genetic mutation that enables fleas to carry it, and which allowed it to infect and kill so many people centuries later.

“To have a close look at the early evolution of this deadly pathogen is really interesting,” says Krause-Kyora. “We see it was more chronic and harmless in the beginning before it became a more deadly disease.”

However, Simon Rasmussen at the University of Copenhagen, Denmark, says the evidence is weak for the claim the plague was milder 5000 years ago. “There are no new results to substantiate these claims and therefore it remains a hypothesis,” he says. Rasmussen also believes the new study doesn’t invalidate the case he and his colleagues put forward in 2018, of the plague driving the Neolithic decline.

“The individual does in fact overlap with the Neolithic decline and very likely died from the plague infection. We know that large settlements, trade and movement happened in this period and human interaction is therefore still a very plausible cause of the spread of plague in Europe at this time,” he says.

Mark Achtman at the University of Warwick, UK, says the team’s interpretations of the plague’s epidemiology appear speculative. “The reasons for epidemic and pandemic outbreaks are unlikely to be found in the bacterial genomes, so ancient DNA of single genomes is not going to help,” he says.

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