The image most people have when they consider the “Black Death” is a large, devastating pandemic that occurred from 1347 to 1353, killing millions of Europeans. However, this is not true; the plague did not disappear after its initial occurrence. It continued to recur over 400 years and continued to change society through repeated outbreaks.
A new study led by the University of Tartu has now pieced together this long history with unprecedented clarity by reading the DNA of the plague bacterium preserved in human remains.
The team sequenced 26 Yersinia pestis genomes from 11 archaeological sites across Estonia, Russia, England, the Netherlands, and Switzerland. These samples span the fourteenth to eighteenth centuries, covering much of the Second Plague Pandemic.
The study shows that there were many times when the plague was introduced into Europe from other areas. The first time was likely through trade routes. This meant that the plague was re-introduced into Europe multiple times as people traveled around the continent.
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These introductions resulted in new reservoirs for the disease and allowed for the development of different genetic variations of the disease. For instance, Estonia had many introductions of the plague over hundreds of years because of its strong connections with the rest of Europe through trade and travel.
A key discovery was the massive growth of plague lineages during the latter part of the 15th Century.
The bacteria divided into three main groups, which may have led to the establishment of new reservoirs within wild rodent populations. Climate might have been a contributing factor: The Great Renaissance Drought could have affected rodent dynamics and caused outbreaks.
“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 Prof.
Kristiina Tambets, senior author of the study.
Unlike modern pandemics, where genome sequences come with precise timestamps, ancient remains are often dated only within broad radiocarbon ranges. To sharpen this picture, the researchers developed a new method that places plague genomes more precisely on the bacterium’s evolutionary tree.
Schematic workflow from data generation to the Phylogenetically Informed Radiocarbon Modeling and historical contextualization. Icons are modified from Flaticon.com. Simplified version of figure from Keller et al. 2026 PNAS.
Author: Keller et al. 2026 PNAS
“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,” explained Dr Marcel Keller, lead author.
The team was able to use this new process to link each of the plague genomes they had access to with an outbreak that had been recorded in writing by a person who was alive at the time; therefore, the team created the first formal system for linking almost all of the known plague genomes from the 14th through 18th centuries with historical records of plagues.
The research indicates that the spread of plague has been influenced by wars. The study demonstrates, using genome analysis, that plague outbreaks occurred as a result of the Thirty Years’ War (1618–1648) and the Great Northern War (approx. 1700–1721).
Soldiers, refugees, and merchants all moved about during these wars and thus contributed to the transmission of plague.
“We see how Yersinia pestis splits into new branches during periods of conflict and spreads along the routes traveled by troops and displaced populations,” said Dr. Christiana L. Scheib, senior author.
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In Tallinn, Plague struck Swedish and Russian troops as well as civilians during the 1710 siege, underscoring how war amplified devastation.
Though Plague is no longer a major threat in Europe, Y.
pestis still survives in rodent reservoirs in parts of the world. Understanding how it persisted for centuries after the Black Death, and eventually disappeared, offers insights into the long-term dynamics of infectious diseases.
Using ancient DNA, archaeology, historical records, and radiocarbon dating, the researchers have created the most extensive genetic record of the Second Plague Pandemic. This research demonstrates that plague was not just one catastrophic event; rather, it was an ongoing threat that continually changed the face of Europe for generations.
This study reminds us that pandemics are rarely one-off events.
They evolve, resurface, and adapt, sometimes for centuries. The lessons drawn from Plague’s long shadow may help us better anticipate and monitor future infectious threats.
Journal Reference:
- Marcel Keller, Meriam Guellil, Philip Slavin and Christina Scheib. A refined phylochronology of the second plague pandemic in Western Eurasia. PNAS. DOI: 10.1073/pnas.2534899123
