Ancient DNA shows plague kept coming back for 400 years after the Black Death

A team led by the University of Tartu has reconstructed 26 ancient genomes of the plague bacterium Yersinia pestis from 11 archaeological sites, tracing how the disease kept returning across Europe for roughly 400 years after the Black Death first swept the continent between 1347 and 1353. The genomes span the 14th through the 18th centuries, covering most of what historians call the Second Plague Pandemic, and the team published its findings in the Proceedings of the National Academy of Sciences.

The point of the project was not to confirm that plague returned repeatedly after the initial catastrophe, which is already well documented in historical records, but to work out where each wave came from and how it kept finding new footholds long after the first outbreak burned through Europe’s cities. Chronicles and parish registers had already established that plague revisited towns across the continent for generations; what they could not establish was whether those later waves were the same lineage smoldering locally or fresh introductions arriving again and again from elsewhere.

Reading 400 Years of Outbreaks in Bone DNA

Researchers pulled ancient DNA from human remains at sites across Estonia, Russia, England, the Netherlands and Switzerland, then combined the 11 newly sequenced genomes with 64 previously published Yersinia pestis genomes to sharpen the dating of outbreaks that were previously known only from vague documentary references. Dr. Marcel Keller, the study’s main author, worked alongside senior authors Prof. Kristiina Tambets and Dr. Christiana Scheib at the University of Tartu, with historian Prof. Philip Slavin serving as corresponding author, according to the EurekAlert release describing the work. A separate summary in ScienceDaily notes the sampled sites were chosen specifically to cover both the earliest post-Black Death decades and the later, less-studied centuries of the Second Plague Pandemic.

Building a usable genome from centuries-old skeletal remains is itself slow, exacting work. Ancient bacterial DNA degrades and fragments over time, and the team had to distinguish genuine Yersinia pestis sequences from contamination before any of the historical questions could even be asked. The full dataset and methodology appear in the team’s PNAS paper, published September 10, 2026.

“[The researchers] 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,” the team reported, describing a pattern of reinfection rather than a single lingering outbreak.

A Three-Way Split Around 1450

The genomes point to a pivotal moment roughly a century after the Black Death. Sometime around 1450 to 1500, the Yersinia pestis lineages circulating in Europe underwent a major expansion and split into three distinct branches, a diversification that researchers say may have let the bacterium establish new rodent reservoirs beyond the ones tied to the original 14th-century pandemic. That branching event, more than any single battle or trade route, appears to explain why plague kept resurfacing in different regions with genetically distinct strains rather than a single unbroken chain of infection.

Estonia’s geography made it a recurring entry point. Long-distance trade connections tied the region to the rest of Europe, and the study’s authors argue those same links that brought goods and travelers into Estonian ports also carried the bacterium back in, again and again, over the following centuries.

Wars That Moved the Bacterium

Two conflicts stand out in the genomic record. The team linked specific outbreaks to the Thirty Years’ War, fought from 1618 to 1648, and to the Great Northern War, which ran from roughly 1700 to 1721, tying disease spikes to the movement of soldiers, refugees and supply lines rather than treating each outbreak as an isolated event.

The 1710 siege of Tallinn supplies one of the clearest case studies. During that siege, plague killed Swedish and Russian soldiers as well as civilians caught in the fighting, a single episode that shows how military campaigns could turn a regional outbreak into a mass-casualty event layered on top of the violence of the war itself.

The researchers also point to the Great Renaissance Drought as a possible contributing factor in the disease’s mid-pandemic expansion, since environmental stress on rodent populations can push infected hosts into closer contact with humans, though the genomic evidence speaks more directly to the war-driven spread than to the climate link.

Refining Dates the Historical Record Left Vague

Much of the study’s contribution is methodological rather than dramatic: a refined approach to radiocarbon dating that let the team tie specific genomes to specific historical outbreaks with more confidence than earlier ancient-DNA work allowed. Coverage from Phys.org and Archaeology News Online Magazine both frame the paper as a corrective to a historical record that documented plague’s return through parish registers and chronicles but rarely connected those written accounts to a specific bacterial lineage.

Ancient Origins notes the study leaves open exactly how many separate reservoirs of the bacterium persisted in European wildlife between visible outbreaks, a question the genomes can narrow but not fully answer. What the 26 reconstructed genomes do settle is that the Black Death was never a single closed chapter — the same pathogen, splitting and re-splitting into new lineages, kept finding its way back into European towns for four centuries after 1353.

This article was produced with the assistance of AI and reviewed by Morning Overview editors prior to publication.

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