The Black Death is often remembered as a single catastrophic event that devastated Europe between 1347 and 1353, claiming the lives of millions of people, but the disease did not disappear after that first devastating outbreak and reappeared in recurring waves for more than four centuries, transforming communities, economies and societies across Europe and beyond.
A new study, led by researchers at the University of Tartu (Estonia) and published in Proceedings of the National Academy of Sciences, sheds new light on this long and complex history by analyzing plague bacteria DNA preserved in archaeological human remains.
The researchers reconstructed 26 genomes of Yersinia pestis (plague-causing bacteria) from 11 archaeological sites in Estonia, England, the Netherlands, Russia and Switzerland. The samples cover a period between the 14th and 18th centuries, and cover much of the so-called second plague pandemic.
The results reveal the complex history of the plague with unprecedented resolution. Instead of persisting in a single place after the Black Death, the disease re-emerged repeatedly in different parts of Europe over several centuries, generating multiple foci of contagion.
Researchers found evidence that the plague was introduced into Estonia on several occasions during much of the second plague pandemic, showing that close connections with other parts of Europe also facilitated the spread of the disease.
One of the most notable findings of the study was evidence of a major expansion of plague lineages around 1450 to 1500, when the bacteria diversified into three main branches that may have established new reservoirs in wild rodent populations.
Researchers speculate that climate changes may have played a role. One possible factor is the Great Renaissance Drought. Recent studies have shown that climate significantly influences plague outbreaks among wild rodents, which act as natural reservoirs of the disease.
"We found evidence of repeated introductions of the plague into Estonia beginning as early as the late 14th century and identified several previously unknown genetic lineages in both urban and rural environments," according to Kristiina Tambets, lead author of the study.
More precise deadline
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 to the Covid-19 pandemic.
During the coronavirus crisis, scientists were able to track the spread of different variants because the genomic sequences came with precise collection dates.
Historical pandemics are different: ancient remains are often only dated within wide radiocarbon intervals that can span more than a century.
"With Covid-19, scientists were able to reconstruct the spread of individual strains with great precision because the genomes had exact time stamps. In the case of historical pandemics, these time stamps are often missing or span more than 100 years, which limits our ability to interpret the genetic data," explains Marcel Keller, lead author of the study.
To overcome this challenge, the research team developed a method that improves the precision and accuracy of those intervals. By analyzing the position of the plague genomes in the bacteria's evolutionary tree, they were able to narrow down the probable dates of many samples and place them in a much clearer historical context.
They subsequently used these improved dates to reevaluate 64 previously published and 11 newly sequenced plague genomes. The result is the first systematic attempt to link almost all currently available plague genomes, from the 14th to the 18th centuries, to historically documented outbreaks.
"We managed to improve the dating intervals of many samples, which allowed us to link them to specific plague waves and outbreaks that were recorded in the respective cities or regions by chroniclers," says Philip Slavin, lead author of the study.
War
The study also underlines the great influence that human activity had on the course of plague epidemics. The newly analyzed genomes provide additional evidence for outbreaks associated with the Thirty Years' War (1618-1648) and the Great Northern War (1700-1721). According to researchers, the plague frequently spread along the same routes used by armies, refugees and traders.
"We observed how the bacteria Yersinia pestis divides into new branches during periods of conflict and spreads along routes traveled by troops and displaced populations," says Christiana L. Scheib, lead author of the study.
