The Black Death of the 14th century: what we really know, thanks to DNA

A few days ago I wrote about the suspected plague case in Irkutsk, in Siberia: a case still full of unanswered questions. The word "plague" alone is still enough to trigger fear today. It is an echo from far away, from the fourteenth century, when a disease arriving from Asia killed an enormous share of Europe's population in just a few years.

You can find anything about the Black Death: wrong dates, invented numbers, anachronistic images, certainties historians do not have. This article tries to do the opposite. It tells what we know, separates what is hypothesis, and above all shows how we know it. Because the great novelty of the last fifteen years is that the Black Death is no longer studied only by historians: it is also studied by geneticists, extracting DNA from the teeth of its victims.

The sources: where our knowledge comes from

Method first. Our knowledge of the Black Death comes from three kinds of sources, each with its limits.

Contemporary chronicles. Valuable testimony, but to be read carefully: many chroniclers wrote from hearsay, exaggerated figures or interpreted events as divine punishment. The most famous Italian account is Giovanni Boccaccio's, who in the introduction to the Decameron describes Florence during the 1348 epidemic.

Administrative records. Tax registers, wills, burial lists, city ordinances. Less evocative than chronicles, but often more reliable for estimating the real impact.

Ancient DNA. The new source, and it has changed the game. In 2010 a study led by Haensch found the bacterium Yersinia pestis in the teeth of victims buried in mass graves in several European countries. In 2011 Bos's team published in Nature the first genome of the bacterium, reconstructed from victims in the East Smithfield cemetery in London (Wikipedia). Since then there has been no doubt about the culprit.

It is the same principle I apply in my work: testimony must always be checked against objective data. I wrote about it with the Farina armour, where a witness's account and museum objects did not match.

Where it began: Lake Issyk-Kul

For more than a century people debated where the Black Death began. China, India, the Central Asian steppes, the Caspian region: every hypothesis had its supporters.

In 2022 a study produced a very strong clue. Researchers analysed two medieval cemeteries near Lake Issyk-Kul, in present-day Kyrgyzstan, at the foot of the Tian Shan range. The tombstones, written in Syriac, showed a spike in deaths from "pestilence" in 1338–1339. DNA extracted from the teeth of seven people buried there contained Yersinia pestis. And the strain found turned out to be the direct ancestor of those that, a few years later, would strike Europe and the Middle East (Wikipedia).

It is one of the rare cases where a funerary inscription and a genetic analysis tell the same story. It does not close the debate completely: some scholars still propose other areas of origin. But today it is the best-documented hypothesis.

The journey to Europe

Caffa, 1346: a story to handle with care

Here enters the most often told story, and the one to handle most carefully. In 1345–1346 the Golden Horde army was besieging Caffa, in Crimea, a Genoese trading colony. According to the Piacenza notary Gabriele de' Mussis, the besiegers, struck by plague, catapulted the corpses of the infected over the walls, infecting the city.

It is one of the stories most cited as the first example of "biological warfare". But historians urge caution: de' Mussis was in all likelihood not present and wrote from others' accounts. And the contagion may have crossed anyway, through rodents and fleas moving across the siege lines. The story is evocative; the proof that it happened that way is not there.

Messina, October 1347

Genoese ships fleeing the Black Sea carried the disease into the Mediterranean. It reached Constantinople in summer 1347. In October 1347 twelve Genoese galleys reached Sicily, and the chronicler Michele da Piazza described their arrival in Messina.

From there the spread was extremely fast:

In less than five years the disease had crossed almost the entire continent, following trade routes by sea and land.

How many died? The honest answer: we do not know precisely

This is where the most invented figures are found. The truth is that there were no censuses in the fourteenth century, and every estimate is a reconstruction. Here are some of the main ones, as reported by Wikipedia:

The range is wide, and not through incompetence: it depends on the sources used and on estimates of the starting population. What is certain is that mortality was enormous and varied greatly from region to region. Anyone giving you a precise number without saying where it comes from is simplifying.

Rats, fleas or people?

The classic account says: black rat, rat flea, human. It is the mechanism by which plague passes from animals to humans, and it is real.

But does it really explain how fast the Black Death crossed Europe? In 2018 Katharine Dean and Boris Schmid, of the University of Oslo, published in PNAS a mathematical model comparing three transmission hypotheses with mortality data from nine European cities. In seven of the nine, the death curve was better explained by transmission through human fleas and lice, that is, between people, than by the rat model (National Geographic).

It is not a final verdict: the authors themselves acknowledge the models can be improved, and the scholarly debate remains open. But it is a good example of how an idea taken for granted for decades can be challenged by data.

Then there is the pneumonic form of the disease, transmitted directly from person to person through respiratory droplets. It is the form discussed in the Irkutsk case, and the most contagious.

Plague and the hunt for a culprit: Basel, 1349

One chapter of the Black Death concerns Switzerland directly, and it is one of the darkest.

Across Europe a rumour spread that Jews were poisoning wells to spread the disease. A wave of massacres followed. In Strasbourg, in February 1349, about 2,000 people were killed. By 1351 dozens of Jewish communities had been destroyed.

In Basel, in January 1349, a mob sanctioned neither by the city council nor by the bishop locked the remaining Jews in a wooden hut on an island in the Rhine and set it on fire. Medieval chronicles speak of 300–600 victims; modern historians consider a number between 50 and 70 more plausible. The children were spared and forcibly baptised (Wikipedia).

The most terrible detail is another: the massacre took place before the plague reached Basel. The city was struck only in spring 1349. The victims were not killed for spreading a disease, but because of a rumour, in a climate of fear.

It is a lesson that still holds today, and one I found almost unchanged in the Irkutsk case: faced with an unknown threat, an unverified rumour quickly turns into a certainty, and someone pays the price.

What the Black Death left behind

Quarantine

One of its most lasting legacies is a word we have come to know well. In 1377 the Republic of Ragusa, today's Dubrovnik, imposed a 30-day isolation on arrivals from plague-stricken areas. The period was later extended to 40 days, and from the Italian for forty comes the word quarantine (Wikipedia).

Traces in our genes

One of the most surprising discoveries is recent. In 2022 a research team led by Jennifer Klunk and Luis Barreiro published in Nature an analysis of 206 ancient DNA samples from people who lived before, during and after the Black Death, in London and Denmark. The study identified immune-system gene variants, in particular in the ERAP2 gene, that appear to have offered greater protection against plague and were therefore favoured by natural selection (McMaster Ancient DNA Centre).

The unexpected twist: some of those protective variants are today associated with a greater susceptibility to autoimmune diseases. In a sense, the Black Death left a mark on our immune system that still endures.

Finding the culprit: a doctor born in Switzerland

Plague did not vanish with the fourteenth century. It returned in waves for centuries, and at the end of the nineteenth century a new pandemic that began in China reached Hong Kong. It was there, in June 1894, that a physician and bacteriologist born in Aubonne, in the canton of Vaud, Alexandre Yersin, isolated the responsible bacterium (Wikipedia). The Japanese scientist Shibasaburō Kitasato was working on it at the same time, and credit for the discovery was long disputed. The bacterium now bears Yersin's name: Yersinia pestis.

Five myths to dispel

"The beaked plague doctor is medieval." No. The beaked costume appears in the seventeenth century, about three centuries after the Black Death, and there is no evidence it was used in the fourteenth (Wikipedia).

"They called it the Black Death." No. At the time people spoke of "pestilence" or "great mortality". The expression "black death" spread much later, through Scandinavian chroniclers of the fifteenth and sixteenth centuries; in English it is attested only from 1755.

"It was all the rats' fault." It is not that simple: as we have seen, person-to-person transmission probably played an important role.

"The Mongols hurled corpses into Caffa: the first biological warfare." Perhaps, but the witness who tells it was probably not there. It is a possible story, not an established fact.

"We know a third of Europeans died." That is one estimate, not a data point. Other scholars reach 60%.

From the fourteenth century to Irkutsk

Back to where we started. The bacterium that killed millions in the fourteenth century never disappeared: it still lives in wild rodent populations in various parts of the world, including Central Asia and Russia, where the Black Death itself began. Between 2019 and 2025 the WHO recorded 2,646 confirmed cases and 423 deaths worldwide, mostly in Congo and Madagascar.

The difference from the fourteenth century is enormous. Today we know what causes the disease, we can diagnose it, and we cure it with antibiotics if treatment starts in time. What has not changed, as both Basel in 1349 and the uncontrolled rumours about Irkutsk show, is the way fear spreads: faster than the bacterium, and with no need for evidence.

That is why, in historical research as in today's investigations, the method remains the same: go back to the sources, separate what is proven from what is merely repeated, and say so clearly.