In the late 14th century, Europe endured one of its darkest chapters: the second Black Death pandemic, which claimed over half the continent's population. To illuminate the origins and evolution of the plague bacterium Yersinia pestis, scientists have sequenced ancient genomes from pandemic-era remains, mapping its path across Europe.
An international team examined remains from ten archaeological sites in England, France, Germany, Russia, and Switzerland. This work sheds light on the second plague pandemic (14th–18th centuries) and the genetic diversity of Yersinia pestis during and after the Black Death.
Published in Nature Communications, the study reconstructs 34 Y. pestis genomes, tracing the bacterium's genetic history to clarify the pandemic's start and spread in Europe.
The second plague pandemic began with the Black Death in the mid-14th century, ravaging Europe and its surroundings until the 18th century and killing nearly 60% of the population. But where did this Yersinia pestis strain originate, and how did it adapt upon reaching Europe?
Though the Black Death looms large in history, its initial entry and spread in Europe have remained elusive due to scarce early outbreak data and limited ancient genomes.
Researchers sequenced plague DNA from the teeth of 34 individuals, including two from Laishevo in Russia's Volga region. They identified a single ancestral strain giving rise to all second-pandemic lineages, with minimal genomic diversity in Black Death samples.
“These results indicate a unique entry of Y. pestis into Europe from the East,” explains lead author Maria Spyrou. “However, future discoveries of unsampled diversity in Western Eurasia may reveal additional insights.”
While the initial European Black Death stemmed from one strain, later-pandemic genomes show a lineage with greater genetic diversity.
“In the later phase of the second pandemic, multiple branches emerged in Europe, suggesting plague persisted in local reservoirs,” notes Marcel Keller. “No modern descendants of this lineage exist, hinting at their extinction.”
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The team also found a deletion in two virulence genes in this second lineage—a feature echoed in extinct strains from the first plague pandemic.
“Since this deletion appears in both extinct pandemic lineages, exploring its effects on human and flea transmission is a key area for future research,” says Kirsten Bos, research group leader at the Max Planck Institute for the Science of Human History.
This research provides fresh perspectives on the pandemic's origins and trajectory, enriching the Y. pestis genomic database. “In-depth analysis of ancient genomes offers unique views into a pathogen's micro-evolution over centuries,” states senior author Johannes Krause.
Future efforts should integrate these findings with disease models, climatology, epidemiology, and historical data to deepen insights into the second plague pandemic.
