The Black Death is best known for the catastrophic wave of plague that swept through Europe between 1347 and 1353, killing millions of people. But the disease did not disappear once the initial disaster passed. The plague returned again and again for more than four centuries, repeatedly disrupting cities, economies and societies throughout Europe and surrounding regions.
A study led by researchers at the University of Tartu now offers a much more detailed look at what happened during those centuries. By analyzing the DNA of plague bacteria preserved in archaeological human remains, scientists were able to reconstruct how the disease spread, evolved and repeatedly reappeared long after the Black Death.
Ancient DNA reveals centuries of plague
The team reconstructed 26 genomes of Yersinia pestisthe bacteria that causes the plague, from human remains recovered from 11 archaeological sites in Estonia, Russia, England, the Netherlands and Switzerland. The samples date from the 14th to 18th centuries and cover a large part of the period known as the Second Plague Pandemic.
Genetic evidence suggests that the plague did not simply survive in one place and spread repeatedly from a single source. Instead, the disease appears to have re-emerged in different parts of Europe over hundreds of years, potentially creating several new reservoirs where the bacteria could persist.
Estonia was hit repeatedly. Researchers found signs that the plague entered the region several times during much of the Second Plague Pandemic, indicating that Estonia’s connections with other parts of Europe also helped the disease spread over long distances.
One of the most striking patterns appeared around 1450-1500. During this period, the plague lineages underwent great expansion and divided into three major branches. Those branches may have helped establish new reserves of Yersinia pestis in wild rodent populations.
Climate may also have influenced this expansion. Researchers point to the Great Renaissance Drought as a possible factor. Studies of modern pest systems have shown that changes in climate can strongly affect outbreaks among wild rodents, which act as natural hosts for the bacteria.
“We found evidence of repeated plague introductions into Estonia starting in the late 14th century and identified several previously unknown genetic lineages, both in urban and rural environments,” said lead author Professor Kristiina Tambets.
Identifying old pest outbreaks
A major challenge in studying historical pandemics is determining exactly when ancient infections occurred.
During the COVID-19 pandemic, researchers were able to track individual variants in remarkable detail because genome sequences were generally linked to precise dates. Samples of ancient diseases rarely contain that kind of information. Archaeological remains are often dated using radiocarbon techniques that can produce time windows spanning many decades or even more than a century.
“With COVID-19, scientists were able to reconstruct the spread of individual strains very well because the genomes came with precise time stamps. In historical pandemics, those time stamps are often missing or can span more than 100 years, limiting our ability to interpret the genetic data,” explained lead author Dr. Marcel Keller.
To address that problem, the team developed a method designed to narrow those wide dating ranges. The researchers examined where individual plague genomes appeared on the bacteria’s evolutionary tree and used that information to refine the likely dates of many samples.
This allowed them to place ancient infections on a much more precise historical timeline.
The researchers then applied the improved dating approach to 64 previously published plague genomes and 11 newly sequenced genomes. Their work represents the first systematic attempt to connect almost all currently available plague genomes between the 14th and 18th centuries to outbreaks described in historical records.
“We were able to improve the dating ranges of many samples, allowing us to connect them to specific plague waves and outbreaks that chroniclers recorded in the respective cities or regions,” said historian and corresponding author Professor Philip Slavin.
The war helped the plague spread through Europe
The genetic record also shows the extent to which human activity influenced the spread of the plague.
Newly analyzed genomes provide additional evidence linking the outbreaks to the Thirty Years’ War (1618-1648) and the Great Northern War (c. 1700-1721). Armies, displaced civilians, refugees, and traders frequently traveled the same routes, creating opportunities for diseases to move between regions.
“We see how Yersinia pestis “splits into new branches during periods of conflict and spreads along routes traveled by troops and displaced populations,” said lead author Dr. Christiana L. Scheib.
The findings add new details to plague outbreaks linked to the Great Northern War. During the siege of Tallinn in 1710, for example, the disease killed Swedish and Russian soldiers, as well as civilians.
Taken together, the evidence shows that the plague was much more than a simple medieval catastrophe. It remained a recurring danger for generations and returned repeatedly to communities across Europe.
Why the plague story is still important
The plague is no longer a major public health threat in Europe, but Yersinia pestis It has not disappeared from the world. The bacteria still persists in natural rodent reservoirs in several regions.
Researchers say that understanding how the plague established itself after the Black Death, remained present for centuries and eventually disappeared from Europe could help scientists better understand the long-term behavior of infectious diseases.
Connecting ancient genomes to recorded outbreaks and possible animal reservoirs can reveal how diseases emerge, spread, establish and persist over long periods. That information could also improve modern disease surveillance and efforts to monitor places where plague still circulates today.
Reconstruction of the second plague pandemic
The project brought together researchers and evidence from various countries and scientific fields. Samples and expertise came from collaborators across Europe, including scientists from the University of Cambridge and research partners from the Netherlands and Switzerland.
Combining ancient DNA analysis, archaeology, historical records and radiocarbon dating, researchers produced what they describe as the most complete genetic picture of the Second Plague Pandemic to date.
The findings reveal a disease that repeatedly crossed borders, evolved into new lineages, followed human movement and continued to shape Europe for centuries after the Black Death ended.