Y is for Yersinia pestis

Burying Black Death Victims in Tournai, Belgium. Gilles Li Muisis, on gavi.org.

We aren’t sure When or Who or Where or How Much. We used to guess about What, although now we seem to be sure. And, when I say we, I do mean scientists and people who study facts and sometimes historians who pay attention to them, instead of making up malarkey.

I’m talking about the Black Death, which I already covered last year in the Renaissance and the letter “B.” And I talked about it in a post on “How do they know?” so why cover it again? Because the key truth about the 14th century plague, the one which devastated Europe and is thought to have come across the Silk Road, is that there are so many unanswered questions.

What: The Digestive System of A Flea

Scientists know a few things about the Black Death. They’ve looked at teeth in the grave of an English cemetery specifically dedicated to the Plague. A landmark study from 2011 reported with strong evidence that the DNA evidence found there by the paleogeneticists was yersinia pestis. That’s bubonic plague. And everybody mentions the study, so it was rock solid science.

They know now what yersinia pestis is; they’ve diagrammed its genome. They know that it’s a pathogen that infects the rodent flea, which works like this. The pathogen infects the flea because it bites an infected rodent. The Y.P. blocks up the flea’s digestive tract, which causes it to bite more because it’s not getting “enough” since digestion isn’t completing its cycle. (A scientist named Bacot actually got to call this the “Bacot block,” which is a little ignominious unless you’re a disease scientist, and you’re thinking Nobel prize. Though I still think it might be odd at cocktail parties…what did you win for? mapping the birth of the galaxy… determining how humans use auctions… advocating for peace in the Rain Forest… isolating the bubonic plague pathogen in the regurgitative cycle of the rat flea….)

The hungry rat fleas at some point eliminate YP back through the esophagus (that’s where the regurgitative cycle comes in) so that they can feed on real blood. That puts the plague into a new host, if the flea has hopped from expired rodent to unsuspecting human. Then the pathogen from the biting flea goes into the circulatory system of the new victim and *pop* go the buboes.

Those smarty-DNA guys mapped out enough of this pathogen to distinguish different types that they believe occurred at different times. In written human history, there are three times where these symptoms were written about as part of a pandemic: 1) Constantinople during Emperor Justinian’s time in the 540s CE; 2) Europe in the 14th century (1330-1380 CE); and 3) China in the 1890s.

DNA Mapping tree of bubonic plague, YP, from Nature.com

Not Enough Rats

So far, so good. They think they know that YP probably caused the Black Death. Well, maybe. They do know that some graves in an English plague cemetery died of YP. They do know other cities had outbreaks with symptoms that describe YP, which are black buboes or lumps on the lymph glands.

There are a bunch problems though: not all cities had outbreaks, the outbreaks came in waves, a lot of places that should have had outbreaks are silent in the historical records, and there weren’t enough rats. The YP–>flea–>rat–>ship–>travel from Asia to Europe–>fleas jump to humans model works fine for one flea or one glob of YP. But it requires an awful lot of rats.

It’s critical to the problem to understand that bubonic plague could not be transmitted from human to human. It could be transmitted if a flea on an infected body jumped to someone in the nearby vicinity; YP could also turn into a pneumatic version and be transmitted in the air. But that didn’t happen often, and the bubonic version doesn’t jump, only the fleas do. And only rat fleas, not the ol’ human fleas that would have been around on the humans.

But wait, there’s more! Problems, that is. The plague outbreaks reoccurred, but mostly in the summer, which didn’t fit when the rats might have traveled or propagated. Because YP can’t jump between humans, that means a lot of rats, an “army of rats” somehow selectively choosing what time of year to stampede into some villages and not others. The confusion about the model has been so acute that other models of potential diseases have cropped up: anthrax or possibly a virus from space.

Who: Gerbils? Marmots? I Thought It Was Rats

Recent studies after the confirmation of the DNA for Y.P. think that perhaps it wasn’t rats in the Middle Ages which were the hosts. Rats were known–and seen–to be the hosts in the bubonic plague which stampeded through China in the 1890s, so much so that cats became hugely valued across Chinese cities. But maybe rats weren’t the source in the 14th century.

One study went looking, not for plague signs, but for signs of some kind of rodent that propagated in the times and places where plague was described. A 2015 study from the University of Oslo thought they found the perfect model: The Gerbil. It turns out that gerbil propagation and die off in Asia rather strongly correlated to the plague outbreaks in Europe. Curiously, the many, many studies that reported on this (some of which erroneously said hamsters, which are not the same species as gerbils) don’t explain the other issue. How did you get so many gerbils on ships or on pack animals?

When & Where: China? Krygzstan? Mongol Empire Saddlebags? What the Hell, Science?

The most curious part of all, from my perspective, is that none of the studies can really pinpoint the origin very well. From a Eurocentric perspective, it’s pretty easy to pinpoint the Mongols throwing a plague-infected body over a wall during the Siege of Caffa, claim biological warfare, visualize Genoese fleeing in ships, and follow the plague to Florence. But the body itself doesn’t transmit the plague (only rats/fleas do) and besides… how did the Mongols get it?

The Chinese 1890 Precious Scroll of the Rat Epidemic, from Harvard.edu.

The quick Eurocentric answer is, Who cares? They’re Mongols and mean doesn’t really cut it. Plus, many of the 20th century writers who described this Asian vector simply stated that it came from China without any evidence that it did. The Chinese did have a bubonic plague epidemic in the 1890s that was caused by rat fleas. There was a rat die-off that had witnesses. There were recorded notes about cats and rats and sad paintings. But the 1890 plague was not the 1340 plague.

Horrors of the plague in Guangdong, from Harvard.edu.

Absence of Evidence is Not
Evidence of

The Chinese did have an epidemic of something in the 1330s. But it’s not described as bubonic or related to rats or fleas. Although it’s long been assumed that death over in the east must have led to death in the west, there’s no description of any movement across Asia. There’s no description of mass 14th century outbreaks in Mongolia, India, or the Middle East. Did the Mongols and the Chinese just never mention it?

Another scientific group just last summer published an article that found more DNA of YP in graves from the 1338. This time it wasn’t in Asia or Europe. It was Kyrgyzstan. This is an area northeast of Samarkand, between Transoxiana and the Tien Shan mountains. It’s near the Silk Road areas where all the traders and travelers in the early 14th century might have been moving. Maybe the location was the key.

Scientist Monica Green thinks the location was the key. Green says that if you look earlier than the 14th century back into the records of the Mongols and other chroniclers, you see outbreaks of plagues mentioned earlier. In her study from 2021, she argues pretty convincingly that ALL of the evidence– ancient DNA, movement of plague across Asia, outbreak records, and flea to rodent to human transmission–is explainable through marmots.

Marmots are plentiful in Asia; nomads shoot them for food the way that Daniel Boone shot rabbits. Marmots do have “rat fleas.” They jump in grain wagons, which travel all over the Tien Shan and Transoxianic passageway in the region. Green thinks that the transmission wasn’t via ships, but either via Mongols carrying flea-ridden marmot in their saddle bags or grain carts carrying the marmots. She says that this is why the DNA strains seem to come back to an origin near the Himalayas.

Monica Green upending the Siege of Caffa model. Photo from Green.

Green’s argument is lengthy, heavily researched, and even proposes how it can be refuted. She describes how the spread of the Mongol empire–and I did not know this a few hours ago when I started writing this post even though I’ve spent the last year studying the Mongol empire–may have spread the disease while they expanded across Asia conquering everything. The spread would have been slow and sporadic, but there is evidence of pandemics described where they had sieges: Baghdad, Qara Khitai, and in the Caucusus.

So it may have been the lowly marmot and riders’ saddlebags or grain sellers sending carts up around the cities and steppes from grain farms. It might have been spreading in the 13th century, not the 14th.

And there’s gotta be a lot of cemeteries in Transoxiana just waiting to have their DNA tested.

3 Replies to “Y is for Yersinia pestis”

  1. How very fascinating! Thank you for this bit of history. And congrats on surviving the challenge, almost done now.

    1. Doing this challenge is so rewarding, although it’s tough to get through the middle of April especially, even if you have it “mapped out.” I’m glad it’s over, but I’m already thinking about next year. Thanks for the comment!

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