Nancy Huang

Mar 24th 2023

Ancient DNA Reveals What Caused the Black Death


The Black Death, a pandemic that swept Europe and Asia in 1346 to 1353, killed much of the population, according to History Today. Outbreaks continued to occur every few generations in Europe, the Middle East, Northern Africa and Asia for the next 500 years.

Despite its huge impact on human history, exactly what caused the Black Death — the original source of the infectious Yersinia pestis bacteria — has been unclear. A recent study published in Nature used ancient DNA to pinpoint the source of the Black Death, offering insights that could help mitigate current and future pandemics, including COVID-19.

A Look Back at the Plague

The plague can be transmitted through airborne particles and the bite of infected fleas, which feed on rats that have long been blamed as the source of the Black Death. The plague bacteria first attack the lymphatic system, causing painful swelling of the lymph nodes in the groin, armpits or neck. This stage is called bubonic plague because of the swollen buboes that ooze pus and bleed.

The infection goes on to cause fever, chills, vomiting, diarrhea and agonizing pain. Without antibiotic treatment, about 60% of patients die, as explained by Frontiers in Microbiology. The bacteria can spread to the lungs and become highly infectious pneumonic plague, which has a mortality rate of 90–95%. It can also spread to the blood and become septicemic plague, which is nearly 100% lethal.

The History of the Black Death

The known history of the Black Death in Europe starts in Crimea, which is a peninsula on the Black Sea. Ships could sail from the Black Sea through Constantinople (now Istanbul, Turkey) and into the Mediterranean Sea to access much of Europe, Northern Africa and the Middle East.

In October 1347, some trade ships from Crimea docked in Sicily. Many of the sailors on board were already dead, and the others were covered in the swollen buboes of bubonic plague, according to HISTORY. The ships were turned away, but the damage was done. The Black Death had entered Europe and would spread by land and by ship, carried by rats and their fleas.

Before the plague arrived in Sicily in 1347, there were stories of a “Great Pestilence” that was ravaging China, India, Persia, Syria and Egypt. The historical records here are less clear, so the origins of the Black Death remained a mystery for 675 years.

Tracing the Source

As reported in Nature, an international team of historians, archaeologists and geneticists headed to Central Asia. This is where Pakistan, Afghanistan and other countries reside north of India, west of China and south of Russia. In present-day Kyrgyzstan, there are two cemeteries that had an unusually large number of burials in 1338 and 1339 and tombstones indicating that the cause of death was “pestilence.”

Could this area have been the source of the Black Death that decimated Europe from 1346 to 1353? By sequencing ancient DNA from these grave sites, the research team was able to confirm the presence of plague. Furthermore, they were able to obtain the complete DNA sequence of the plague bacteria responsible for those deaths and compare it to other DNA sequences for Y. pestis.

The previously identified DNA sequences fall into four major groups, which are the result of a “Big Bang” mutation event associated with the start of the Black Death. The ancient DNA sequence fit perfectly at the base of the plague family tree. These results provide good evidence that the source of the Black Death was in Central Asia.

Plague Reservoirs Are Keeping the Bacteria Alive

Plague is not primarily a disease of humans and would die out if there were only human hosts. However, plague bacteria survive within wild rodent populations around the world in so-called plague reservoirs. Therefore, the “pestilence” noted on ancient tombstones in present-day Kyrgyzstan must have come from a plague reservoir if it was truly what caused the Black Death. Indeed, researchers found that the ancient plague DNA sequence closely matches the sequence of Y. pestis found recently in nearby wild rodent populations.

The presence of animal reservoirs makes it nearly impossible to completely irradiate plague. According to the World Health Organization, there are still cases of plague every year, mostly in Africa during the epidemic season. Luckily, antibiotics now provide an effective treatment.

The Death Tolls of 3 Major Pandemics

In Europe from 1347 to 1352, the Black Death killed an estimated 25–30 million people out of a population of 80 million, according to World History. That’s around 30–40% of the European population. It’s estimated that the Black Death was responsible for an additional 25 million deaths in Asia and North Africa, as explained in National Geographic.

For comparison, the 1918 flu pandemic claimed an estimated 17.4 million lives (.95% of the worldwide population at the time), according to the most recent (2018) estimates by Spreeuwenberg et al. as reported by Our World in Data.

As of February 2023, COVID-19 has caused more than 6.5 million deaths in a global population of 8 billion people (0.23% of the global population), according to the World Health Organization. This number is based on 7.5 million deaths officially attributed to COVID-19 and an estimate of unreported deaths.

Lessons for COVID-19 and Future Pandemics

Just as plague reservoirs allow plague to return to healthy populations, viral reservoirs are of grave concern for COVID-19. The virus that causes COVID-19 can infect a variety of animals, including bats, white-tailed deer, farmed mink and domestic cats and dogs.

As explained in Nature, viral reservoirs could be the source of new variants of COVID-19, such as the highly infectious Omicron variant. The Omicron variant has an astonishing 50 mutations compared to the original virus that emerged from Wuhan, China. What is truly remarkable is that these 50 mutations were not detected gradually — despite sequencing millions of COVID-19 samples — but showed up in the tested population all at once. A leading theory is that Omicron evolved in an animal reservoir, such as rats, and was then transmitted to humans.

Experts agree that the next pandemic is inevitable and that the only question is when. As such, it would be wise to gain a better understanding of the source of infectious diseases today so we can better protect against them tomorrow.

Are you interested in all things related to science and technology? We are, too. Check out Northrop Grumman career opportunities to see how you can participate in this fascinating time of discovery.