A TEAM OF researchers from France, Sweden and Denmark have identified a new strain of Yersinia pestis, the bacteria that causes plague, in DNA extracted from 5,000-year-old human remains. 

The analysis, published in the Cell journal, suggests that plague may have been spread among Neolithic European settlements by traders, contributing to the settlements’ decline at the dawn of the Bronze Age.

Their work also suggests that this strain is the closest ever identified to the genetic origin of the plague. 

“Plague is maybe one of the deadliest bacteria that has ever existed for humans. And if you think of the word plague, it can mean this infection by Y pestis, but because of the trauma plague has caused in our history, it’s also come to refer more generally to any epidemic,” said senior author Simon Rasmussen, a metagenomics researcher at the Technical University of Denmark and the University of Copenhagen.

“The kind of analyses we do here let us go back through time and look at how this pathogen that’s had such a huge effect on us evolved.”

New strain

To better understand the history of the plague, Rasmussen and his team examined genetic data from ancient humans, screening for sequences similar to more modern strains of plague. 

They found a strain they had never seen before in the genetics of a 20-year-old woman who died around 5,000 years ago in Sweden. 

The strain had the same genes that make the pneumonic plague deadly today and traces of it were also found in another individual at the same gravesite – suggesting that the young woman did likely die of the disease.

This strain of the plague is the oldest that’s ever been discovered. 

The researchers were also able to determine that it’s also the most basal – meaning that it’s the closest strain we have to the genetic origin of Y pestis. It likely diverged from other strains around 5,700 years ago, while the plague that was common in the Bronze Age and the plague that is the ancestor of the strains in existence today diverged 5,300 and 5,100 years ago, respectively.

This suggests that there were multiple strains of plague in existence at the end of the Neolithic period.

Spread of plague

Rasmussen also believes that this finding offers a new theory about how plague spreads.

Massive human migrations from the Eurasian steppe down into Europe are known to have occurred around 5,000 years ago, but how these cultures were able to displace the Neolithic farming culture that was present in Europe at the time is still debated.

Previous researchers have suggested that the invaders brought the plague with them, wiping out the large settlements of Stone Age farmers when they arrived.

However, if the strain of plague the researchers found in the Swedish woman diverged from the rest of Y pestis 5,700 years ago, that means it likely evolved before these migrations began and around the time that the Neolithic European settlements were already starting to collapse.

At the time, mega-settlements of 10,000 to 20,000 inhabitants were becoming common in Europe. This made job specialisation, new technology and trade possible. They also may have been the breeding ground for plague, the authors suggest. 

“These mega-settlements were the largest settlements in Europe at the time, ten times bigger than anything else. They had people, animals and stored food close together, and, like, very poor sanitation. That’s the textbook example of what you need to evolve new pathogens,” Rasmussen. 

We think our data fits. If plague evolved in the mega-settlements, then when people started dying from it, the settlements would have been abandoned and destroyed. This is exactly what was observed in these settlements after 5,500 years ago. 

 Plague would also have started migrating along all the trade routes made possible by wheeled transport, which had rapidly expanded throughout Europe in this period.

Rasmussen goes on to suggest that the plague would have arrived through these trade interactions at the small settlement in Sweden where the woman his team studied lived. 

He argued that the woman’s own DNA also provides further evidence for this theory – she isn’t genetically related to the people who invaded Europe from the Eurasian steppe, supporting the idea that this strain of plague arrived before the mass migrations did.

Limitations

The researchers note that there are some limitations to what the data from the study can determine. 

It’s important to note that the researchers have not yet identified the plague in individuals from the mega-settlements where it may have evolved. 

“We haven’t really found the smoking gun, but it’s partly because we haven’t looked yet. And we’d really like to do that, because if we could find plague in those settlements, that would be strong support for this theory,” Rasmussen said. 

 Regardless, he believes that this study is a step toward understanding how plague – and other pathogens – became deadly.