Black Death: Ancient DNA gives clues to bubonic plague's 'ground zero'

• The Black Death plague killed millions of people over the course of 500 years.
• Its point of origin has been debated and misattributed ever since, according to a new study.
• The study narrows down the Black Death’s emergence to two ancient graveyards in modern-day Kyrgyzstan.

People naturally don’t like waiting for answers to troubling questions, and the recent rush to pinpoint the origin of SARS-CoV-2 — and to assign blame for the pandemic — is a case in point.

However, science takes time. Sometimes a long time. A new study, for example, finally pinpoints the source of the 500-year bubonic plague, more widely known as the Black Death, that broke out nearly 700 years ago.

The study traced the origin of the Black Death to a pair of cemeteries in the Chüy Valley near Lake Issyk-Kul in modern-day Kyrgyzstan, a former Soviet republic.

The Black Death was caused by the bacterium Yersinia pestis. It first reached a port in Sicily in 1347, where it went on to kill up to 60% of the western Eurasian population in just 8 years, working its way across the continent. In that first wave from 1334-1353 Black Death is believed to have killed 75-200 million people.

It went on to kill millions more in frequent outbreaks across the globe in what is called the “Second Plague Pandemic” over 500 years. It wasn’t until 1896 that the first effective treatment, antiserum, was discovered.

As with SARS-CoV-2, the Black Death was believed by many to have started in China, with some sources still incorrectly listing the country as its point of origin.

The study was published in Nature.

Sequencing the past

The two cemeteries, Kara-Djigach and Burana, were excavated from 1885 to 1892. Examination of tombstones revealed an extraordinary number of deaths in 1338 and 1339, with some attributed to an unspecified pestilence.

According to the study, the inscription on one tombstone can be translated as:

“In the Year 1649 [1338 AD], and it was the Year of the Tiger, in Turkic Bars. This is the tomb of the believer Sanmaq. [He] died of pestilence [“mawtānā”].“

Combining genetic fragments extracted from the skeletons and teeth of seven individuals, five from Kara-Djigach and two from Burana, the authors of the study were able to construct four genomes robust enough to confirm the deceased were genetically consistent with residents of the local area.

Most importantly, three of the seven individuals showed evidence of Y. pestis DNA, confirming that the local “pestilence” was the Black Death.

The genetic timing

It has long been believed that the Black Death’s rampage through Eurasia was accompanied by an explosion of genetic diversification into roughly four branches.

Two of the genomes in the study represented a single strain of Y.pestis that the study characterizes as “the most recent common ancestor of a major diversification commonly associated with the pandemic’s emergence.”

Lead author Dr. Maria Spyrou told Max-Planck-Gesellschaft that they found that the ancient strains from Kyrgyzstan were “positioned exactly at the node of this massive diversification event.”

Study co-author Dr. Philip Slavin told Medical News Today:

“Genetic diversification is still a very poorly understood phenomenon. To get a good grasp of this phenomenon, much research into plague ecologies needs to be done — something that plague historians and scientists should be prioritizing.”

The location

Plague bacterium thrives in rodent “plague reservoirs,” and this particular region provides a plausible venue for zoonotic transfer.

Senior author Professor Dr. Johannes Krause says, “We found that modern strains most closely related to the ancient strain are today found in plague reservoirs around the Tian Shan mountains, so very close to where the ancient strain was found.”

“Changes in the environment and climate can affect reservoir populations like wild rodents, either by decimating them or by causing their increase in size. In both cases, this can cause spillover events, which can in turn trigger epidemics,” Dr. Spyrou told MNT.

A strain from the Justinian plague that preceded the Black Death was also found in the region. Although Dr. Spyrou noted that “it is more than 200 years older than the first documented [Justinian] outbreaks of AD 541.”

“So,” said Dr. Slavin, “one thing we can say is that it appears that the Tian Shan region may have had centuries-old, perhaps millennia-old, plague reservoirs, housing-related plague branches and strains — strains related to the Kara-Djigach strain.”

The right answer requires patience

“Our current abilities in making precise connections between the past and the present are extremely important in understanding how infectious diseases emerge, which types of hosts are involved in their emergence, how they disseminate among human populations, and what factors have determined their present-day distribution and diversity,” said Dr. Spyrou.

Rather than hurrying to a quick solution, a more expansive approach is wise, according to Dr. Slavin:

“It is important to see how these diseases develop evolutionarily and historically, it’s always important to not treat different strains as isolated phenomena, but as something that is situated within a much wider evolutionary picture.”

“To understand the phenomenon of emerging epidemic diseases, it is essential to have as ‘bigger’ [an] evolutionary picture as possible.”
— Dr. Philip Slavin

“And to understand how they develop and [get] transmitted,” Dr. Slavin added, “it is important to consider the environmental and socio-economic history contexts, in which these processes happen.”

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