The researchers reconstructed 26 genomes of Yersinia pestis, the bacterium responsible for plague, from 11 archaeological sites in Estonia, Russia, England, the Netherlands, and Switzerland. The samples span a period from the fourteenth to the eighteenth centuries, covering much of the so-called Second Plague Pandemic.

The results reveal the complex history of plague with unprecedented resolution. Rather than persisting in a single location after the Black Death, plague repeatedly resurfaced in different parts of Europe over several centuries, seeding multiple new reservoirs. 

One of the study's most notable findings was evidence of a major expansion of plague lineages around 1450–1500. During this period, the bacterium diversified into three major branches that may have established new reservoirs in wild rodent populations.

The researchers speculate that climatic changes could have played a role. One possible factor is the Great Renaissance Drought. Modern studies have shown that climate strongly influences plague outbreaks among wild rodents, which serve as natural reservoirs of the disease to this day.

War helped spread disease

The study also highlights how strongly human activity shaped the course of plague epidemics. Newly analysed genomes provide additional evidence for outbreaks associated with the Thirty Years’ War (1618–1648) and the Great Northern War (c. 1700–1721). According to the researchers, plague frequently spread along the same routes used by armies, refugees and traders.

One example for that are the burials from Domat/Ems (Canton of Grisons, Switzerland), which were excavated around the church of Sogn Pieder. “We found several burials with two to four individuals and we noticed an overrepresentation of young men. Grave goods and remains of military equipment gave the hint that they might be victims of a plague epidemic during the “Bündner Wirren”, a side theatre of the Thirty Years’ War” said Cantonal archaeologist Dr. Thomas Reitmaier.

The researchers were able to reconstruct complete genomes from two plague victims, showing a close relationship with plague genomes from other sites dating to the Thirty Years’ War. Interestingly, the next closest relative was not found in one of the sites in the French or Italian Alps but in Brandenburg an der Havel.

“We see how Yersinia pestis splits into new branches during periods of conflict and spreads along the routes travelled by troops and displaced populations,” said senior author Dr Christiana L. Scheib.

The findings offer new insights into plague outbreaks during the Great Northern War. In Tallinn, for example, plague caused casualties among Swedish and Russian troops as well as civilians during the 1710 siege.

More broadly, the research shows that plague was not a single historical disaster but a recurring threat that devastated cities and regions generation after generation.

“We found evidence for repeated introductions of plague into Estonia starting already in the late 14th century and identified several previously unknown genetic lineages, both in urban and rural settings” said senior author Prof. Kristiina Tambets. “The youngest genomes come from burials associated with the siege of Tallinn in 1710, dug for civilians as well as Swedish and Russian soldiers.”

More precise timeframe

One of the most innovative aspects of the study was a new method for assigning historical plague outbreaks to recovered plague genomes. The importance of this approach can be illustrated by comparing it with the COVID-19 pandemic. During the coronavirus crisis, scientists were able to track the spread of different variants because genome sequences came with precise collection dates. Historical pandemics are different: ancient remains are often dated only within broad radiocarbon intervals that can span more than a century.

“With COVID-19, scientists could reconstruct the spread of individual strains extremely well because the genomes came with precise timestamps. For historical pandemics, those timestamps are often missing or may cover more than 100 years, which limits our ability to interpret the genetic data,” explained the main author, Dr Marcel Keller, currently a research fellow at the Department of Environmental Sciences, University of Basel. “To overcome this challenge, we developed a method that improves the precision and accuracy of those intervals. By analysing the position of plague genomes on the bacterium's evolutionary tree, we were able to narrow down the likely dates of many samples and place them into a much clearer historical context.”

The researchers then used these improved dates to reassess 64 previously published and 11 newly sequenced plague genomes. The result is the first systematic attempt to link nearly all currently available plague genomes from the fourteenth to eighteenth centuries with historically documented outbreaks.

“We were able to improve dating intervals for many samples, which allowed us to connect them to specific plague waves and outbreaks that were recorded in the respective towns or regions by chroniclers,” said historian and corresponding author Prof. Philip Slavin.

Why it matters today

Although plague is no longer a major public health threat in Europe, the disease has not disappeared. Yersinia pestis causes yearly casualties in Asia, Africa, North and South America, where the contagion survives in natural rodent reservoirs.

The researchers argue that understanding how plague established itself after the Black Death, persisted for centuries, and eventually disappeared from Europe can help scientists better understand the long-term dynamics of infectious diseases.

By linking ancient plague genomes to historical outbreaks and potential reservoir populations, the study provides new insights into how pandemics emerge, spread and persist over time. Such knowledge may also contribute to modern disease surveillance and public health efforts aimed at monitoring contemporary plague foci.

Collaboration across countries and disciplines

The study was made possible through extensive international collaboration. Samples and expertise came from partners across Europe, including researchers at the University of Cambridge and collaborators in the Netherlands and Switzerland. By combining ancient DNA research, archaeology, history, and radiocarbon dating, the team has produced the most comprehensive genetic picture of the Second Plague Pandemic to date and provided new insights into how one of history's deadliest diseases shaped Europe for centuries.

Link to the paper: https://www.pnas.org/doi/10.1073/pnas.2534899123