On Aug. 27, 2025, for the first time an interdisciplinary team at the University of South Florida (USF) and Florida Atlantic University (FAU), with collaborators in India and Australia, identified Yersinia pestis, the microbe that causes plague, in a mass grave at the ancient city of Jerash, Jordan, near the pandemic’s epicenter. The groundbreaking find definitively links the pathogen to the Justinian Plague marking the first pandemic (AD 541–750), resolving one of history’s long-standing mysteries.

For centuries, historians have deliberated on what caused the devastating outbreak that killed tens of millions, reshaped the Byzantine Empire and altered the course of Western civilization. Despite circumstantial evidence, direct proof of the responsible microbe had remained elusive — a missing link in the story of pandemics.

Two published papers led by USF and FAU provide these long-sought answers, offering new insight into one of the most consequential episodes in human history. The discovery also underscores plague’s ongoing relevance today: while rare, Y. pestis continues to circulate worldwide. In July, a resident of northern Arizona died from pneumonic plague, the most lethal form of Y. pestis infection, marking the first such fatality in the U.S. since 2007, and just last week another individual in California tested positive for the disease.

Genomic analysis revealed that the plague victims carried nearly identical strains of Y. pestis, confirming for the first time that the bacterium was present within the Byzantine Empire between AD 550-660. That genetic uniformity suggests a rapid, devastating outbreak consistent with historical descriptions of a plague causing mass death.

A companion study, also led by USF and FAU, places the Jerash discovery into a wider evolutionary context. By analyzing hundreds of ancient and modern Y. pestis genomes — including those newly recovered from Jerash — the researchers showed that the bacteria had been circulating among human populations for millennia before the Justinian outbreak.  

The team also found that later plague pandemics, from the Black Death of the 14th century to cases still appearing today, did not descend from a single ancestral strain. Instead, they arose independently and repeatedly from longstanding animal reservoirs, erupting in multiple waves across different regions and eras. This repeated pattern stands in stark contrast to the SARS-CoV-2 pandemic (COVID-19), which originated from a single spillover event and evolved primarily through human-to-human transmission. 

Together, the landmark findings reshape the understanding of how pandemics emerge, recur and spread, and why they remain a persistent feature of human civilization. The research underscores that pandemics are not singular historical catastrophes, but repeating biological events driven by human congregation, mobility and environmental change — themes that remain relevant today.