26 Plague Genomes Rewrite What Happened After the Black Death

The Black Death did not end in 1353. A new genetic study of medieval and early modern burials shows that the bacterium behind it kept changing for centuries, and that a major shift may have come around 1450 to 1500, long after the first wave had passed.

The research, published in the Proceedings of the National Academy of Sciences, was led by the University of Tartu in Estonia. The team reconstructed 26 genomes of Yersinia pestis from human remains at 11 archaeological sites in Estonia, Russia, England, the Netherlands and Switzerland. The samples span the 14th to the 18th centuries, the period historians call the Second Plague Pandemic.

What the study found

Between roughly 1450 and 1500, the bacterium diversified into three major branches. According to the researchers, some of these lineages may have established new reservoirs in wild rodent populations. If so, that would help explain how plague kept returning to European towns generation after generation, rather than burning out after the first wave of 1347 to 1353.

The study also links the genetic record to human events. The new genomes add evidence for outbreaks associated with the Thirty Years' War (1618 to 1648) and the Great Northern War (about 1700 to 1721). The authors say plague often travelled along the same routes used by armies, refugees and traders. Genomes from Estonia point to repeated introductions of plague from the late 14th century onwards.

The drought question

The drought link needs careful handling. The researchers suggest that the Great Renaissance Drought, a period of severe dryness in Europe, may have played a part. Their reasoning rests on modern studies showing that climate strongly influences plague among wild rodents and the fleas that carry it. This is a hypothesis. The study does not show that drought caused the branching. The diversification itself comes from the genome data, while the climate explanation remains speculation.

There are other limits. Most of the genomes come from northern and western Europe, so the picture is uneven. Dating has improved but still carries uncertainty. The identity of any 15th-century rodent reservoirs is unresolved, because ancient animal hosts rarely preserve recoverable plague DNA. For readers who want the mechanics of how the disease moved between rodents, fleas and people, our guide to Black Death causes and transmission covers the ground.

Dating the dead

One reason the study matters is method. Ancient burials are usually dated by radiocarbon, and the resulting ranges can span more than a century, which makes it hard to tie a genome to a specific outbreak. The team developed an approach called Phylogenetically Informed Radiocarbon Modelling, which uses a genome's position on the bacterium's family tree to narrow the date range.

Professor Philip Slavin of the University of Stirling, a co-author, said this allowed the team to connect samples to plague waves recorded by local chroniclers. The researchers then applied the improved dates to 64 previously published genomes and 11 newly sequenced ones, in what they describe as the first systematic attempt to link nearly all available plague genomes from the 14th to 18th centuries with documented outbreaks.

Why it matters for medieval history

For England, the study is a reminder that the plague years were not a single catastrophe. Recurring outbreaks kept pressing on a population that had already lost a huge share of its people. Our overview of the Black Death in medieval England sets out the first wave, and the debate over the death toll shows how hard the human cost is to measure even for those years. Later waves matter because they may have slowed any recovery, and the wider social and economic consequences of the plague were shaped by its repeated return, not only by 1348 and 1349.

The findings also bear on how we name things. The disease that killed millions in the 14th century and the plague that persists in rodent populations today share a causative organism, but the terms are not interchangeable, as we explain in Black Death versus bubonic plague.

What comes next

The authors say more samples are needed, especially from southern and eastern Europe and from ancient rodent remains that could identify reservoirs directly. Plague still circulates in wild rodents in parts of the world today, and the researchers argue that understanding how it settled into animal populations after the Black Death may help modern disease surveillance.

Source: Study published in Proceedings of the National Academy of Sciences (doi.org/10.1073/pnas.2534899123); University of Stirling press release, 11 September 2026; Nature World News, 22 September 2026.

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