Every infection leaves a trace. The traces we notice at the moment are social, as we move away from each other and try to step back to avoid the touch of COVID-19. But some traces are physical, deeply imprinted in the antibodies and genetic histories we carry around in our bodies. And they remain, sometimes long after we have gone.
As little as ten years ago, the traces that historians were trained to detect to write histories of the great pandemics of the past were entirely documentary: the records that people at the time kept of the horrors they had never imagined would overwhelm their societies, and for some of these writers, even themselves. On the basis of such written evidence, we reconstructed these pandemics. They could be gripping in the way only human dramas can be. I still recall the excitement of reading Plagues and Peoples, a global history of the plague that William McNeill published in 1976, when I was a student. I was blown away by the scale on which he worked, tracing the Black Death forward from the fourteenth century and all across the world in one grand sweep.
That book is all the more impressive today for the fact, from where my generation of historians now sits, McNeill wrote it blind. He made terrific use of the abundance of mediaeval diaries, reports, and laments chronicling the painfully human evidence of infection and death. But he didn’t have access of what has recently dropped into our laps and made all the difference to the global histories of disease we now write: genomic science. Genetic research has put that work on an entirely new footing. Just as pandemics change the history of the world, genomics have changed how we write it.
Genomic sequencing is what makes this possible. This process identifies the particular string of molecules that constitutes the genetic code of every living organism and that distinguishes it from every other. Complex organisms, like humans and plague bacteria, have DNA, which we visualize as a double helix of two strands of molecules bonded to each other in pairs. COVID-19 is a virus, a much simpler organism. It has RNA, a stripped down version of DNA in which the molecular code is arranged along a single strand. RNA or DNA, it doesn’t matter. These are the ticker tapes that tells every organism who or what it is, and genomic analysis now makes it possible to read those tapes.
And so historians have entered the story. Our general task is to account for the ways in which humans have responded, collectively and individually, to the circumstances that nature and other humans have created for them. We want to know how people in the past have lived and died, and what ties us to them. In the matter of their deaths, we used to read the wills, burial registers and pathologist reports that chronicled some of that experience. We attended to the descriptions that the living kept as kin and friends died. But we looked only from outside the body. We had no other place to stand.
Thanks to biogenetics, all this is changing. Because every infection leaves a physical trace in the body, we can now go inside. Mostly these traces disappear as we do, but not all. Certain data-rich parts of the body have a chance of surviving decay, and these are the parts that palaeogeneticists, as they are now called, work on. Bones are good starter material, because their marrow preserves traces of the DNA of the pathogens that have wracked the body. The best material of all, though, are teeth. Their tough enamel coating means that the snapshot traces of our epidemiological history that linger in dental pulp have been better preserved there than in any other body part. Teeth are what plague geneticists go looking for, like relic hunters of the past, though in their case, the search is for the secrets of our earthly lives, not the promises of our lives to come. To my surprise when I first started looking at plague burials, teeth survive intact in large numbers. This is for the simple reason that our mediaeval ancestors didn’t have sugar. People regularly died with a full set of healthy teeth in their heads, a distinction I forfeited decades ago.
The European practice of plague burial in the Middle Ages supplies us with a huge archive in which to dig. One of the best is the plague cemetery in East Smithfield, London. When between a third and a half of the city’s residents died in the plague of 1348, the bishop of London needed a place to dispose of the corpses. He hallowed a patch of ground to the east of the Tower of London and buried them there. When the site was redeveloped in the 1980s, the remains of 762 bodies were discovered and excavated. Rather than being disposed of, they were put into storage with the thought that perhaps one day they might reveal something to future science. As indeed they have. The big breakthrough came in 2011. A team of scientists headed by Kirsten Bos at the Ancient DNA Centre at McMaster University announced that they had sequenced the plague genome from teeth in the East Smithfield horde. The mystery surrounding whether the plague as we know it today is the same as the Black Death was solved: with minor variations, it is.
Soon more burials around Europe were excavated and more genomes sequenced. As this happened, differences in their genomes came to light. This allowed scientists to sequence the reproduction of the plague as it moved around western Eurasia. The differences that were detected derive from the only purpose pathogens such as the plague or the coronavirus have, which is to reproduce as fast as they possibly can. For them, the meaning of life is simply to create more of themselves. Perhaps that’s the meaning of life for every species, but let’s set that thought aside. Reproduction may be the purpose of life, but it is also life’s most unstable moment. Sometimes, very rarely, the duplicating process goes wrong, and the duplicate contains a glitch, a tiny error. When this happens in the case of the plague, one of the four and a half million pairs of molecules strung along the plague genome switches from one type to another. A distortion this tiny does not alter the organism’s basic nature. But it leaves a trace in the genome’s sequence, because every mutation is permanent and passed along in the next duplication. Once one of these changes (called a polymorphism, or a “change in form”) has happened, it can’t be undone. Every subsequent copy, every future duplication, must include the glitch. Stumbling from glitch to glitch is about the most concrete way to express what evolution is.
If we ever needed proof that time is an arrow, this is it. Once a polymorphism happens, the DNA can’t go backward in time and reverse it. It can only carry the glitch forward. Once the glitches have been identified, it is not difficult to put their genomes in temporal order, one genome begetting another. The result is a family tree in which grandpa’s evolutionary peculiarity gets passed down to each subsequent generation. Putting a family tree together gives us the history of an outbreak. To go back to the Black Death, the DNA recovered from East Smithfield differs by only two glitches from the DNA recovered from Barcelona. In turn, plague DNA from a recent excavation in Bolgar City, briefly a Mongol capital up the Volga River, is just one polymorphism different from the London DNA. The changes got passed down the line. The DNA IN Barcelona glitched before it got to London, and London got glitched when it went up the Volga. Regardless of what the documents might or might not say, the bodily remains tell us that this wave of the plague moved from Barcelona to London and then up the Volga, tracing a curioulys circular movement that carried the disease back into the Mongol zone from which it first emerged.
This may be stating the obvious, but a pathogen doesn’t move unless people do. The plague can drift about among rodent populations, but it can’t cover more than fifteen kilometers a year. The coronavirus couldn’t manage a kilometer without our involvement. In other words, viruses and bacteria don’t cause pandemics; they merely exploit whatever opportunities are on offer, whether that is a plane ride to the next international airport or a boat ride up the Volga.
Pathogens lead simple lives and tell simple stories. It is we who complicate the picture. Pandemics are us.
This is why historians love pandemics. They show people in motion. Showing that, they show us how places and people across the world were connected to each other long before anyone dreamed of our version of globalization. Modern transportation systems and the systems of global greed we decorate with the name of supply chains have given us the means to speed up the process, but otherwise it’s still the same story. Well, not quite. Modern medicine has given us the technologies of vaccination and intensive-care treatment to which our ancestors had no access. Even though some of us will die, we in 2020 are the lucky ones. Without these technologies, the current outbreak of COVID-19 might well be chalking up fatality rates to match the Spanish flu a century ago, or even the Black Death another six centuries before that. But this is not good enough to congratulate ourselves. The medical science has improved, but our social policies haven’t. For the elderly, for the marginalized, those without access to medical care, the outcome will not be kind. The fact that bodies will not be piling up outside city gates is a reprieve of sorts. We would do well to use this reprieve to begin learning about the interconnectedness of us all, and acting accordingly.
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