How scientists cracked the 1,500-year-old plague that reshaped an empire

For the first time, scientists have found genetic proof of the plague bacterium Yersinia pestis in a 1,500-year-old mass grave in Jordan, confirming its role in the deadly Justinian pandemic

Scientists have cracked a 1,500-year-old medical mystery. For the first time, researchers have recovered genetic evidence of Yersinia pestis, the plague bacterium, from a mass grave in Jerash, Jordan.

 

The findings, published in the journal Genes under the study Genetic Evidence of Yersinia pestis from the First Pandemic, confirm that the Plague of Justinian (AD 541–750), the world’s first recorded pandemic, was caused by the same microbe behind the Black Death that swept across Europe and Asia from approximately 1346 to 1353, killing an estimated 25 to 50 million people in Europe alone.

 

The researchers recovered plague DNA from a mass grave in Jerash, Jordan, placing the deadly bacterium right at the empire’s heart for the first time. The findings also reveal that pandemics like this do not come from one single source but keep re-emerging from hidden reservoirs across the globe.

 

What did scientists discover in Jerash?

Archaeologists unearthed a mass grave beneath the ancient hippodrome of Jerash, a city near Amman, Jordan. Inside were the remains of nearly 230 people, including men, women, and children, buried hastily around AD 550–660.

 

Using advanced DNA sequencing and proteomics, researchers found genetic traces of Yersinia pestis in the teeth of multiple victims. All the victims carried nearly identical strains, suggesting a sudden, devastating outbreak of a single lineage.

 

This is the first genetic evidence of plague from the Eastern Mediterranean, right next to the historical epicentre in Egypt, where the Justinian Plague was first documented.

Why is this discovery such a big deal?

Until now, plague DNA from the First Pandemic had only been detected in far-flung parts of Europe like Germany, France, Spain, and England, thousands of kilometres away from Jordan. That left a gaping hole in the story.

 

The Jerash evidence finally confirms that the pathogen was present at the heart of the empire and also explains why written accounts describe terrifying waves of mortality and entire cities being overwhelmed. One of Jerash’s grandest civic structures, its Roman circus, was even converted into a mass grave, a haunting reminder of how societies scrambled to cope with sudden catastrophe.

‘Plague did not emerge once, but resurfaced from hidden reservoirs’: Researchers

The researchers also found that the plague bacterium had multiple origins, not one, and that pandemic strains did not descend from a single ancestor but emerged independently from deep, local reservoirs across Eurasia. The study found:

• Dormant but deadly: The bacterium often lay “asleep” in animals or soil for centuries, only to resurface in humans during times of dense trade and travel.
• Human-driven evolution: During pandemics, plague spread so fast through cities and trade routes that humans themselves became “evolutionary engines” for the pathogen.

In short, plague wasn’t a one-off disaster but a repeating ecological event, shaped by human societies and their connections.

How is this different from Covid-19?

According to the researchers, plague and Covid-19 pandemic followed very different evolutionary paths. Covid-19 came from a single spillover event (likely in late 2019) and spread rapidly via human-to-human transmission, with variants evolving in a predictable timeline.

 

Plague, on the other hand, keeps re-emerging in multiple places and times from ancient reservoirs like rodents, fleas, and even soil. Its genetic “clock” doesn’t tick neatly like viruses; instead, it pauses and restarts depending on outbreaks and environmental conditions.

Could plague still be a threat today?

The study says it is a possibility. Though rare, plague has not disappeared. A recent case in Arizona led to the US’s first pneumonic plague death since 2007. Just a week later, another case was reported in California. Globally, plague remains endemic in regions like Madagascar, Central Asia, and parts of Africa.

 

India, too, has faced the disease in recent memory. The city of Surat in Gujarat witnessed a major outbreak in 1994, when pneumonic plague cases triggered panic, mass migration, and international concern. While the outbreak was swiftly contained, it remains one of the most striking reminders that plague is not just a relic of history but a modern public health challenge as well.

 

As Dr Rays H Y Jiang of the University of South Florida, one of the lead authors, explained in a statement on the website of USF Health News, University of South Florida:

 

“We have been wrestling with plague for a few thousand years, and people still die from it today. Like Covid, it continues to evolve, and the threat will never go away.”