The plague epidemic known as the Black Death devastated Europe from 1347 to 1353, killing millions of people. It is often viewed as a single historical event that came and went. In reality, the plague did not disappear after its first devastating outbreak. Over the next five centuries, the disease returned to Europe again and again, having a major impact on communities and reshaping cities and trade routes.

A new study led by the University of Tartu's Institute of Genomics provides a highly nuanced picture of the plague's long and complex history. Researchers analyzed genetic material from plague bacteria found in the remains of people who lived between the 14th and 18th centuries. Using this material, they mapped how the plague spread, evolved and persisted across Europe, including Estonia, during the period that began with the Black Death and continued afterward, known as the second plague pandemic.

The plague was also a frequent uninvited visitor to Estonia

The study reconstructed 26 genomes of the plague bacterium Yersinia pestis. The samples came from individuals who lived hundreds of years ago and were recovered from 11 archaeological sites in Estonia, Russia, England, the Netherlands and Switzerland.

The results show that the plague did not reach Estonia just once. The disease was repeatedly introduced into the country throughout nearly the entire second plague pandemic. Researchers also discovered previously unknown lineages of the plague bacterium and found genetically almost identical strains in different locations. This suggests that plague outbreaks spread very rapidly across Europe through contacts between different regions.

One of the most notable findings was evidence that the plague bacterium underwent genetic diversification between approximately 1450 and 1500. During this period, the bacterium split into three major branches that established new reservoirs of infection among wild rodents.

The researchers believe climate change may have played a role. One possible factor they cite is the so-called Great Renaissance Drought of 1540. Modern studies have shown that climate has a significant impact on the spread of plague among rodent populations, which serve as natural reservoirs for the disease.

"We found evidence that the plague repeatedly reached Estonia as early as the late 14th century and we identified several previously unknown genetic lineages of Yersinia pestis in both urban and rural areas," said Kristiina Tambets, one of the study's lead researchers and professor of archaeogenomics at the University of Tartu.

New method for dating historical outbreaks

One of the study's key innovations was the development of a method that allows ancient disease outbreaks to be placed on a timeline much more precisely. According to the authors, a comparison with the Covid-19 pandemic helps illustrate the method's significance.

Study author Marcel Keller said researchers tracked the spread of different variants of the virus during the coronavirus pandemic by analyzing their genomes. "Because the samples had precise dates, it was possible to reconstruct the spread of the virus almost in real time. With historical epidemics, such precise 'timestamps' are usually unavailable and dates obtained using the widely used radiocarbon dating method can span more than a century," Keller explained. This degree of uncertainty makes it difficult to link specific finds to particular historical disease outbreaks.

To address this problem, the research team developed a method that combines genetic and archaeological chronological information. Using an evolutionary tree constructed from plague bacterium genomes, the researchers were able to determine the age of many samples more precisely based on their position on older or younger branches of the tree. This also allowed the samples to be linked to specific historical events.

In addition to sequencing the new genomes, the researchers used the new method to analyze 64 previously published plague bacterium genomes. This is the first systematic attempt to link most known plague genomes from the 14th to 18th centuries to plague outbreaks documented in written sources.

The new approach allows ancient DNA data to be used much more effectively to study the spread of epidemics. It also makes it possible to reconstruct, with a high degree of chronological precision, events that affected Europe over centuries as successive waves of plague swept across the continent.

Wars help diseases spread

The findings also show how strongly human activity and historical events influenced the spread of the plague. The study also confirms that later plague outbreaks repeatedly reshaped the course of history.

The study adds to existing knowledge with new plague genomes linked to the Thirty Years' War (1618–1648) and epidemics during the Great Northern War (approximately 1700–1721). Genetic evidence suggests that the plague often spread as a result of wars and military campaigns.

"We can see how Yersinia pestis evolved during military conflicts, split into new lineages and traveled along the same routes as troops, refugees and trade," Marcel Keller said. During the 1710 siege of Tallinn, for example, the plague claimed lives on both sides, including Swedish and Russian soldiers as well as civilians.

More broadly, the study shows that the plague was not a single catastrophe but a recurring threat lasting for centuries, devastating cities and regions generation after generation.

Why plague research remains relevant

Although the plague no longer poses a significant health threat in Europe, the disease has not disappeared from the world. Yersinia pestis continues to persist in wild rodent populations in several parts of the world.

Understanding how the plague became established in Europe after the Black Death, persisted for centuries and eventually receded helps researchers better understand the long-term dynamics of infectious disease transmission. Such knowledge also supports modern efforts to monitor and prevent infectious diseases.

The study was the result of extensive international collaboration. Ancient DNA researchers worked closely with Estonian archaeologists and anthropologists studying the history of the plague in what is now Estonia, as well as researchers at the University of Cambridge and partners in the Netherlands and Switzerland.

The collaboration combined ancient DNA research, archaeological and historical data and radiocarbon dating to create the most comprehensive genetic picture of the second plague pandemic to date. It also provided new insights into how one of history's deadliest diseases shaped Europe's development over the course of centuries.

The study was published in the Proceedings of the National Academy of Sciences.

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