On Pandemics: Deadly Diseases from Bubonic Plague to Coronavirus

For two great teachers of veterinary epidemiology—the late John Iversen, who inspired me to care about the dead skunk in the middle of the road, and Wayne Martin, who taught me to measure its significance

From ghoulies and ghosties

And long-leggedy beasties

And things that go bump in the night,

Good Lord, deliver us!

A traditional prayer, of unknown provenance

Contents

1 An Introduction to the Second Edition

2 Threats, Outbreaks, Epidemics, and Pandemics: A Primer

3 Zoonoses and Diseases People Get from Other Animals

4 Plagues, Rats, and the Perfection of Fleas

5 Lyme, with a Twist

6 Biting Flies, Kissing Bugs, and Sleeping Sickness

7 Western Equine Encephalitis, Television, and Air Conditioning

8 West Nile Virus and the St. Louis Blues

9 The Chickens Fight Back, with Ducks

10 Queens of the South: Nipah, SARS - COV , and SARS - COV -2

11 Rats, Bats, and Monkeys: Lassa, Ebola, and Marburg

12 Splashing through Rat Piss: Leptospires and Hantaviruses

13 All the Rage

14 Abortion in the Sandbox and Other Pet Problems

15 Poker Players’ Pneumonia

16 Bang’s Disease and the White Plague

17 Dog Parasites in the Land of the Gods

18 Stories for the InterPandemic

selected readings

acknowledgments for the second edition

index

( 1 )

An Introduction to the Second Edition

I WROTE THE first edition of this book in the turbulent wake of avian influenza’s spectacular appearance in the late 1990s, and the even more dramatic SARS alarm early in this century. In quite different ways, both diseases awakened fears and memories of the 1918 influenza pandemic, and led to widespread animal slaughtering, airport closings, government panic, mayoral rants, and rock concerts. On the other hand, the pandemic of influenza that swept around the world in 2009 and 2010, first called swine flu, and later given the technical moniker H1N1, evoked measured responses accompanied by widespread skepticism.

In 2020, I am writing this second edition of the book during a global lockdown in response to the explosive spread of SARS-COV-2 (the virus) and COVID-19 (the disease it causes). COVID-19 has now joined the list of pandemics, near-pandemics, and possible pandemics that have long haunted human history. With popular names such as SARS, bird flu, swine flu, Ebola, and bubonic plague, these diseases all have one thing in common: they are zoonoses, diseases that have made the jump from their natural homes in other animals to take up residence in people. Some of them—the influenzas, mostly—took the direct route from chickens or pigs to people. Others, such as Ebola, COVID-19, and SARS, took a more circuitous route from bats, pausing at rest stops in one or two other animals—civets, monkeys, or pangolins, perhaps—before they found their way to humans. Welcome to the twenty-first century.

The eruption and worldwide spread of SARS-COV-2 was, some might assert, predictable, but predictable only in the sense that earthquakes and volcanic eruptions in certain parts of the world are predictable. The Ring of Fire, for instance, home to more than three-quarters of the world’s volcanoes, is a horseshoe-shaped area rimming the Pacific Ocean. We can predict that there will be volcanic eruptions and earthquakes along this rim, but exactly where and when they will occur is uncertain.

There were reports, of course, briefings, warnings about emerging infectious diseases, rumors of chimeric viruses that bore traces of their animal origins. In retrospect the reports should have been heeded; they weren’t just angry jeremiads. They were based on scientific studies and simulations. But there were events other than rogue viruses in a Chinese market that kept us distracted. And in our collective distraction and denial, we were surprised. I could say we shouldn’t have been surprised, but I’ve never found retrospective told-you-sos to be comforting or useful.

Even the most scientifically literate among us might be forgiven our skepticism that an outbreak led by an unstable, albeit crowned, virus, was going to usher in a New Age, or even a Different Age. Some might argue, based on good evidence, that crowned heads have always been somewhat unstable. On the other hand, we wouldn’t be the first to have underestimated the impact of a small event—say, a butterfly flapping its wings in Brazil on storms in Texas. The world is more chaotic, less predictable, than we would like to believe.

Many of the pandemics imagined in movies and novels before 2020 involved apocalyptic scenarios that included people stumbling through garbage-strewn streets, bleeding from all orifices, zombies, billions dead, and bodies in the street. Perhaps a few religious or ideologically obsessed zealots even wished, mostly in secret, for one of those God-save-us pandemics that historian Walter Scheidel announced might provide a sufficiently violent shock to upend the established order and flatten disparities in income and wealth.

What most literary scenarios did not imagine was an infection that spread rapidly, infected hundreds of thousands, and seemed to kill almost at random. Of course, as with previous pandemics, COVID-19 has tended to kill more older people, and people whose immune systems were already under duress from cancer or diabetes or heart disease. But what has struck many observers, myself included, was how two healthy people in the prime of life could be infected with SARS-COV-2, and one of them, without any reasonable medical explanation, would die, while the other lived. This almost seemed like the random drive-by shootings described by my Colombian colleagues from the 1990s.

So, yes, the SARS-COV-2 pandemic was predictable, but as one of my Italian colleagues, in lockdown as I write this, said, Even in the case of an earthquake, whilst the earth is shaking, the first reaction (seconds or less) is denial: it is impossible, it cannot be true, not here! And even afterward, when you see the ruins, it’s still hard to believe.

Most of us have been made aware of the ravaged landscapes, lost habitats, and disappearing megafauna that have characterized the past century. We fret about the extinctions of birds and rhinos. We try to save some arthropods, like bees and butterflies, even as we try to kill others, like mosquitoes. Still, even the most conservation-minded among us rarely think about the trillions of viruses, yeasts, fungi, and bacteria for whom these disappearing animals are home, or about where those microfauna might look for new homes once we raze their habitats for mines, cattle ranches, or cities. The diseases described in this book are, in a sense, about microscopic refugees from those lost habitats and disappearing species.

The living things on this planet are one big, dysfunctional extended family of species, in which most bacteria, viruses, and parasites are beneficial and necessary, in which diseases have a useful role in nature, and in which we ourselves have evolved from microbes and are composed of them. I think we—this big family, including the bothersome and wonderful and contradictory human species—can work out our problems with the help of some serious narrative therapy. War, with all its calls to arms, technological weapons, and national pride, its suspension of civil liberties, xenophobia, and collateral damage, is often used as a metaphor for how we should fight disease. But that is too impoverished and small-minded an image. Perhaps politics, the so-called art of the possible, is a better metaphor. War is a last resort.

After millennia of war on the agents of disease and the eradication of some of the worst, we might even find ways of negotiating with them, of accommodating each others’ needs, engaging in minor, stylized skirmishes, with a reasonable, acceptable death toll on all sides. In the twenty-first century, we are discovering that we will have a common future, or none at all. But such a future will require us to educate ourselves in different, more ecologically aware, ways. One of our many tasks is to translate that education into a new version of common sense, a kind of solidarity with other people, and other species, informed by careful attention to this amazing planet we share.

Clinical neurologist Oliver Sacks has argued that we do not honor our peripheral vision as much as we should. Sacks was talking about his own individual experience, but some of us have argued that the highly focused-but-disoriented stumbling about of biomedical sciences reflects a collective lack of honoring—indeed, a pathological loss—of peripheral vision.

If epidemiologists of human diseases were more aware of animal diseases, if veterinary epidemiologists spent more time having conversations with public health officials, if economists and politicians were more aware of complex social-ecological webs, if every upstart business guru were more aware of the unintended consequences of disruptive entrepreneurial innovations, if we were as good at paying attention to the world around us as we are to what is just in front of us . . . then maybe we would not have been so shocked by the appearance of COVID-19. Those are a lot of ifs, none of which can be addressed by any single profession or scientist or politician; peripheral vision in the global sense requires us to watch out for each other. In an overcrowded twenty-first-century world, we are each other’s peripheral vision.

We will all die. That is a normal part of life. Still, there are ways to make our dying more pleasant, less catastrophic, more as if we are among mortal friends. As the poet W.H. Auden once wrote: The slogan of Hell is to eat or be eaten; the slogan of heaven is to eat and be eaten.

If we understand just a little more about the animals we share this planet with and the micro-organisms that they carry around, both those that we eat, and those that will eat us, we might even begin to understand ourselves.

FINALLY, BEFORE WE step into the butterfly-induced tornado of terminology related to outbreaks, epidemics, and pandemics, I should say something about names. If the names of hurricanes are open to criticism, the names of diseases are even more fraught. The task of naming things, whether in upper-class European Latin from the seventeenth century, or in popular culture, is a very human burden. This task is not to be undertaken without careful thought. In some cases, careless naming has led to reckless blowing up of bat caves and slaughtering of civets or dogs. Naming a disease after where it was first found (West Nile, Lagos, Hong Kong, Asian, Russian, Wuhan) might provide useful shorthand for field investigators—or an opportunity for demagogic, xenophobic, and racist rants. A name can hinder the implementation of good public health programs. H1N1 was called swine flu, until several leaders in the Middle East, understandably offended, suggested that it be called the Mexican virus. Virologists settled the matter with a name that sounds like a postal code for an address in another, parallel, world. At other times, after someone, whether thoughtlessly or maliciously, labeled a disease according to ethnicity, sexual orientation (e.g., HIV as a gay disease), nationality, or economic status, millions of people have been stigmatized, ostracized, assaulted in the streets, and murdered. In this book I shall, insofar as is possible, use technical scientific names and, where these are not available or are too obtuse, descriptive popular names, such as SARS (severe acute respiratory syndrome).

( 2 )

Threats, Outbreaks, Epidemics, and Pandemics: A Primer

UNTIL A few years ago, many scientists had banished words like threat and danger from our vocabulary. In an attempt to be more rigorously quantitative and less emotional, we began to write about risks. Our response to danger was called risk management. A risk is a threat or a danger that you put into a box. Then you can count boxes, and manage them. The assumption in risk management is that you can quantify danger. This is only partially true.

Epidemiologists sometimes define an epidemic as more cases than they would expect, or as unusually high rates. But measuring this isn’t as simple as it sounds. We can ask, first of all, whether in our case numbers we are counting people exposed to a virus (and who may be test-positive), people who have been infected but don’t show any clinical disease, people who are clinically ill, or people who die. We might, if we are the World Bank and are worried about economic impacts, try to calculate disability-adjusted life years; that is, how many years of economically productive life are lost. This means that the younger you are when you get sick, the greater the impact (assuming you are economically productive).

Once we decide who and what to count, we are faced with another set of questions. What are we referring to when we say expected or usual? That is relatively easy, at least from a scientific point of view. The expected or usual numbers are those we’ve seen over the past few decades. Even if the numbers of cases are unexpected or unusual, however, we need to ask: Are we dealing with a disease that is important?

How do we assess importance? Is it a scientific decision? Are authorities more hesitant to use the loaded word pandemic for some diseases, preferring to speak of a global epidemic of AIDS or high rates of malaria or diarrhea in certain parts of the world? If so, why is that? Do some diseases so radically and explicitly expose global economic inequities that the wealthy owners of global institutions would prefer to focus on those that more directly threaten Europe and North America and for which a technical, money-making fix is more likely to be found? Hey, I’m a curious epidemiologist. I’m just asking. The truth is that although words like outbreak, epidemic, and pandemic have a scientific ring to them, and some grounding in science, their use is very political.

Now, after decades of quantitative risk management, in the new age of emerging infectious diseases such as bird flu, SARS, Ebola virus disease, and COVID-19, we seem to be back in a jungle of threats and dangers. If SARS-COV-2 has taught us anything at all, it’s that even our best quantitative, scientific measurements cannot give us all the answers we want.

Before we dive into what we mean by a pandemic—that equivalent to the man-eating lion in the dark forest—let me begin the definition with something smaller, at least in terms of numbers: an outbreak. An outbreak occurs when a relatively small group of people or animals or plants gets sick, as when everyone gets sick after eating a warm potato salad on a sunny day. The source of an outbreak can usually be traced to one particular event or exposure.

The next step up from an outbreak is an epidemic, which is like an outbreak, only huger. The word epidemic goes at least as far back as Homer, in about the eighth century BC. Homer used it to refer to someone in his or her own country, as differentiated from a traveler. It had connotations of indigenous or endemic. Hippocrates, in 430 BC, gave it a medical slant, referring to physical syndromes (illnesses) that occurred in particular places and times. After the discovery of bacteria in the nineteenth century, people began to use the term to refer to specific diseases, as in epidemics of cholera. More recently, the word has been used to refer to more cases than expected, both of very specific diseases, such as hemolytic uremic syndrome caused by E. coli O157:H7, and general syndromes, such as obesity.

This brings us back to the question of expectations. Every year, we expect a certain number of cases of say, influenza A. When we get more than we expect, or we are faced with a new variation of the same old thing, we call it an epidemic. Some diseases, such as West Nile virus disease and Lyme disease, start as epidemics. They surprise us. But after a few years, we get used to them, and we think of them as troublesome, tiresome, endemic. They now belong here, wherever that here may be. The words we use to describe these disease patterns are both descriptive and a way to catch—or divert—our attention. Why, some might ask, are there more cases than we expect? How and why have our expectations changed?

Multi-country outbreaks of various strains of food-borne Salmonella, noroviruses, and E. coli are regularly reported around the world. These are rarely called epidemics. And almost never called pandemics. These are the normal costs of producing lots of food, or so we are led to believe. If nothing else, the language we use should tell us something about our expectations in the twenty-first century.

Pandemics are a step beyond epidemics, at least in terms of numbers. The World Health Organization (WHO) defines a pandemic as an epidemic occurring worldwide, or over a very wide area, crossing international boundaries and usually affecting a large number of people. The classical definition includes nothing about severity: a disease may become pandemic without being a serious killer. A serious killer disease, even one appearing in many different parts of the world, may not necessarily be classified as a pandemic.

SARS, for instance, was never officially declared a pandemic. Our global alarm was that it might become a pandemic, and was intensified by a general confusion about the non-human origins of most human diseases. Similarly, HIV/AIDS spread around the world in ways that some of us could only describe as a pandemic. In fact, although many agencies and researchers do call it a pandemic, WHO refers to it as a global epidemic. Before 2020, the only WHO-declared pandemics since 1900 were in 1918, 1958, 1968, and 2009. All were influenza, and all our guidelines for pandemic response are based on influenza.

If you find this confusing, you are not alone.

Influenza viruses afflicting millions of people annually cross international boundaries in temperate southern and northern hemispheres. However, these seasonal epidemics are not called pandemics. An influenza pandemic is a global outbreak of a new influenza A virus, such as the H1N1 strain associated with the 2009–10 pandemic. According to the Centers for Disease Control and Prevention (CDC), "Pandemics happen when new (novel) influenza A viruses emerge which are able to infect people easily and spread from person to person in an efficient and sustained way. This is why, when pandemics are first described, we often see the word novel or variant or just a little n or v" in front of the name.

In 2009, WHO published a document called Pandemic Influenza Preparedness and Response, which offers more specific guidance. This guidance document described a model with six pandemic phases. The model starts with Phase One, in which other animals, but no people, are infected, and finally arrives at Phase Six, the Pandemic Phase, in which there is increased and sustained [human-to-human] transmission in the general population. To be considered a true pandemic, however, this human-to-human transmission can’t just be inside one country, or even in two countries in the same WHO administrative region, but must also be in at least one country in a different administrative region.

After that, waves of the disease go around the world, but fewer people get sick and die with each subsequent wave, either because humans have built up immunity or because the agent, defying creationists, evolves through the processes of mutation and natural selection. In this case, only those with milder forms of the disease survive long enough to pass it on to others, and hence the agent moves in with our species to a longer, gentler, more sustainable life.

In 2017, WHO published another guide, called Pandemic Influenza Risk Management. This guide is not a planning document. It is intended to manage disaster risks and to help countries assess risks so that they can make more informed decisions. This document, which appears to be the one that WHO used during the SARS-COV-2 pandemic, only shows four phases: Interpandemic, Alert, Pandemic, Transition and then—wait for it, another Interpandemic phase. Note that this document assumes that whenever we are not in a pandemic, we are between pandemics, as we are between ice ages. Although they were designed to manage influenza in humans, WHO phases can be applied to all infectious diseases. There is no non-pandemic phase in our future. We have always lived between pandemics and we always will.

I will remind you (and me), here, that the word pandemic does not imply severity. The emergence of H1N1 in pig populations and its spillover into humans appeared, at least at first, to be an example of this. In 2009 this new influenza virus was reported from Mexico and spread very rapidly into an officially declared global pandemic in just a few months. For both scientists and just plain folks, the whole thing was befuddling. Was this serious? Was it real? First bird flu. Now swine flu. Really?

To the relief and puzzlement of many, the new virus seemed to result in a human disease no more, or less, serious than the normal flu. Admittedly, normal influenza infects millions and kills thousands annually. Still, when, in June 2009, WHO declared that the spread of H1N1 was a pandemic, some of us were less than alarmed. When virologists were able to rapidly incorporate the novel virus into the annual flu vaccination package, I actively supported vaccination programs. My general view of vaccinations is that they are there more to protect others than to save myself. Whatever side effects the vaccine might incur were part of my commitment to keeping the people around me and in the community healthy. I believed then—as I still do—that many anti-vaxxers are driven by selfishness. As an admittedly privileged, and sometimes smug, white male Canadian, this me-me-me business was not something to which I aspired. Still, I had my moments of cynicism. Even as WHO explained pandemics to the general public, and rolled out their six-phase pandemic preparedness plan, I devised my own version of the phases of what I called pandemic panic. My categories started at a pre-panic Phase One, a kind of who-cares phase, in which infection was transmitted among animals in poor countries, then moved into an early panic phase, characterized by moral outrage, in which European and North American tourists returned home with stories about sick dogs or children in the streets. The highest levels of panic and depression among European and American officials, who usually lead the charge on responding to these emerging diseases, involved sick wealthy white people and corporate financial losses on the stock market.

By August 2010, when the pandemic was declared over, and WHO announced that H1N1 had settled into the typical seasonal patterns, the new virus had officially killed 18,500 people. The mathematical models used to follow seasonal influenza suggested actual deaths from H1N1 ranged between about 150,000 and 575,000. These numbers are not those we might find with Ebola, but they are not trivial.

On the face of it, the why questions of the H1N1 pandemic appeared, at first, to be straightforward. The initial explanation was that the virus originated in commercially raised pigs in Mexico. Later, based on comparisons between the genetic composition of the 2009 virus and other swine influenza viruses circulating in the region, researchers discovered that the movement of viruses from Eurasia and the United States into Mexico closely followed the direction of the global trade of live swine.

Pigs were raised in large-scale operations in Mexico for the North American market for reasons similar to those used for large-scale poultry production. Mexico (and many other countries) offered somewhat relaxed labor laws and low-cost workers. An infected farm worker, receiving low wages and with no paid sick leave or health insurance, would have every incentive not to stay home even when seriously ill. Under these inequitable social and labor conditions, the virus would have been transmitted back into the pigs in a positive feedback cycle. An obvious measure to prevent the spread of the virus would have been for all countries importing pigs from these farms to require them to have paid sick leave and health insurance for their workers, and to meet minimum standards of hygiene.

In one sense, every death is expected and tragic. Optimism about technological breakthroughs notwithstanding, death is, and will remain, the usual course of events. The world could not unfold as it should if we did not all, sooner or later, die. This eventuality is what gives us despair even as it opens