Ancient plague genome recovered from sheep remains

Scientists have extracted the genome of an extinct strain of plague from the remains of a 4,000-year-old domesticated sheep. Livestock may have played a significant role in the spread of plague, which circulated across Eurasia during the late Neolithic and Bronze Age, according to a study published in Cell.

Around 5,000 years ago, the contemporary form of the plague spread across Eurasia but disappeared 2,000 years later. Genetic studies have shown that the strain of this ancient plague—LNBA Yersinia pestis (Late Neolithic and Bronze Age)—could not have been transmitted by rodent-borne fleas, as is typical of modern strains of the disease. Wild animals must therefore have been responsible for its spread. Scientists believe it spread from this as-yet-undetected reservoir to sheep and other farm animals, subsequently increasing the risk of human infection.

Most human pathogens originate from zoonotic sources. Growing evidence also indicates that many infectious diseases emerged within the last 10,000 years, a period coinciding with the domestication of animals. The rise of livestock farming may have led to increased contact between humans and wild animals, which serve as reservoirs for pathogens such as the LNBA Yersinia pestis.

To investigate how the plague spread across Eurasia over the millennia, an international team of researchers from the Max Planck Institute of Infection Biology (MPI IB), Harvard University, the University of Arkansas, the Max Planck Institute of Evolutionary Anthropology (MPI EVA), and Seoul National University examined the bones and teeth of Bronze Age farm animals at the Arkaim site in Russia, a site belonging to the pastoral Sintashta-Petrovka culture.

Thanks to this research, scientists have identified for the first time the LNBA strain of Yersinia pestis in a 4,000-year-old animal—a domesticated sheep. The results of the study were published in Cell (DOI: 10.1016/j.cell.2025.07.029).

"The Arkaim site is an excellent place for such research. These were early pastoral societies that did not use grain storage facilities, which prevented them from attracting rats and, therefore, fleas. Traces of Y. pestis infection have been found in members of this culture before," said Dr. Taylor Hermes, professor of anthropology at the University of Arkansas and co-author of the study.

Comparison of the fossil LNBA Y. pestis genome from sheep with other genomes showed that it was nearly identical to the genome of a pathogen that infected humans at the same time. Therefore, humans and animals were infected with the same LNBA Y. pestis population.

In other regions where Y. pestis is still endemic, it is known that sheep can become infected through contact with dead infected rodents, which are the natural reservoir of the pathogen.

This could cause localized outbreaks of plague in humans if the sheep were not properly dressed. A similar scenario may have occurred in prehistoric times.

"The Sintashta-Petrovka culture was famous for grazing cattle on vast pastures, which created many opportunities for livestock to come into contact with wild animals infected with LNBA Y. pestis. From there, it was only one step to human infection," said Dr. Christina Warinner of Harvard University and MPI EVA.

Unlike present-day lineages that show geographic variation, the ancient LNBA Y. pestis was similar throughout its range of almost 6,000 km.

As the scientists explained, their next task will be to find this unknown primary reservoir of prehistoric plague bacilli. The search for pathogens in fossil animal remains is just beginning, and excavations could yield thousands of animal bones. Much material from previous studies also awaits reanalysis.

Ewelina Krajczyńska-Wujec (PAP)

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