Pandemic: Tracking Contagions, from Cholera to Coronaviruses and Beyond

by Sonia Shah

between 1940 and 2004, more than three hundred infectious diseases either newly emerged or reemerged in places and in populations that had never seen them before.

And so I set off for the slums of Port-au-Prince, the wet markets of south China, and the surgical wards of New Delhi, in search of the birthplaces of pathogens old and new.

Wet markets are open-air street markets where vendors sell live animals captured from the wild to consumers to slaughter and consume. They service the Chinese taste for what’s called yewei, or “wild,” cuisine,

It was in a wet market in Guangzhou that the virus that nearly caused a pandemic in 2003 was born. This particular virus normally lived inside horseshoe bats. It was a kind of coronavirus, a family of viruses that mostly cause mild respiratory illnesses.

From the horseshoe bats, it had spread into other wild animals caged nearby, including raccoon dogs, ferret badgers, snakes, and palm civets. As the virus spread, it mutated. And in November 2003, a mutant form of the horseshoe bat virus started infecting people.

Like other coronaviruses, the virus colonized the cells lining the respiratory tract. But unlike its more mild brethren, the new virus tinkered with the human immune system, disrupting infected cells’ ability to warn neighboring cells of the viral intruder in the body. As a result, in about a quarter of the infected, what started off seeming like flu rapidly escalated into life-threatening pneumonia as infected lungs filled with fluid and starved the body of oxygen. Over the following months, the virus sickened more than eight thousand with what came to be known as SARS, for severe acute respiratory syndrome. Seven hundred and seventy-four people perished.

The SARS virus vanished after that. Like a brightly burning star, it used up all its available fuel, killing people too quickly to spread any farther.

From cows, we got measles and tuberculosis; from pigs, pertussis; from ducks, influenza.

The road from animal microbe to human pathogen was turning into a highway.

At some point—nobody knows just when—a microbe of bats, the filovirus Ebola, started to spill over and infect people. In humans, Ebola causes hemorrhagic fever and can kill 90 percent of those it infects.

Monkeypox is a virus that lives in Central African rodents. It comes from the same genus of viruses as the now extinct variola, the virus that caused smallpox, which killed between 300 and 500 million people over the course of the twentieth century.

forest destruction, more people live in and around the monkeypox-infected rodents of Central African forests.

The growing size of pig farms in Malaysia had similarly allowed a bat virus called Nipah to spill over into people. As pig farms in Malaysia have grown, they’ve increasingly abutted the forests where bats roost. This allows bats and pigs to come into novel, intimate contact.

The pigs’ troughs are situated near the fruit trees where bats roost. When bat excreta drop into those troughs, the pigs are exposed to bat microbes. At one particularly large pig farm, Nipah virus sickened so many pigs that it was able to spill over into the local farmers, killing 40 percent of those infected. Nipah virus also struck in South Asia and now erupts in Bangladesh nearly every year, killing 70 percent of the afflicted.

West Nile virus is a flavivirus of migratory birds named after the district in Uganda where it was first isolated in 1937. Migratory birds have probably been introducing the virus into the United States for decades, especially into New York City, which lies on the Atlantic flyway, one of the four primary migratory routes in North America. The virus can spill over from birds’ bodies into ours when mosquitoes bite infected birds and then bite people.

But avian biodiversity, like the biodiversity of other species, has plummeted, in the United States as elsewhere. Urban sprawl, industrial agriculture, and climate change, among other disruptions caused by human activity, steadily destroy bird habitats, reducing the number of species among us.

But as the suburbs grew in the Northeast, the forest was fragmented into little wooded plots crisscrossed by roads and highways. Specialist species like opossums, chipmunks, and weasels vanished.

When the opossums and the chipmunks disappeared, tick populations exploded.

Pigs harbor MRSA. They pass it on to their handlers, and the bacteria appear in their slaughtered flesh sold at the supermarket, although whether people get infected from eating it is still an open question.

A University of Iowa study found that 3 percent of meat samples collected from Iowa grocery stores carried MRSA. In the Netherlands, the strain of MRSA commonly found among pigs causes 20 percent of MRSA infections in humans.54

Thanks to the miracle of air travel, one infected man seeded a global outbreak.

most bacteria in Indian hospitals are gram-negative, which means they are encased in tough outer membranes that make them more resistant to antibiotics and antiseptics than the gram-positive strains that dominate in Western hospitals.

does not regulate the use of antibiotics (they’re widely available across the country without a prescription), many of India’s bacterial pathogens are impervious to antibiotics.

Penny-pinching vendors commonly diluted the milk they sold with water, and in cheap dives, bartenders diluted the alcoholic drinks with water, too. When New Yorkers drank their hot teas and coffees with water-diluted milk, or consumed diluted cocktails, they could get a deadly dose of cholera.36 (While a 20 percent gin cocktail killed cholera vibrio in an hour, a 15 percent gin cocktail wasn’t strong enough for the job.)

Whole families perished from cholera.

Like human excreta, dog poo teems with pathogenic microbes, such as strains of E. coli, roundworms, and other parasites. One of the most common parasitic infections in Americans is the result of their exposure to dog feces.

As a result, livestock produce thirteen times more solid waste than the human population does in the United States.55 To cope with the tens of millions of gallons of excreta they produce, farmers mix it with water and then pump it into untreated, multi-acre cesspools (“manure lagoons”). This wastewater is sprayed on crops, but since local croplands can’t absorb it all, it leaches into the groundwater and runs off into the surface waters.

The nature of the urban landscape spelled the difference. “When it gets into the cities,” he said, “then it takes on another dimension.

When infected victims die, their bodies will be abandoned, burned, or buried—possibly before the pathogens lurking inside can spread to anyone else. This is a serious disadvantage. And it’s why highly virulent strains are more likely than less virulent ones to die out.

Virulence is evolutionarily constrained. But certain human behaviors lift these brakes on virulence, allowing even the most deadly strains to flourish. One example is burial rituals that require the bereaved relatives to handle the corpses of their loved ones.

Virulence doesn’t handicap their ability to spread, because they can spread from their dead victims by persisting in the environment until another live victim picks them up.

Pathogens that spread through social contact are usually destined to be relatively mild. Crowds allow even these pathogens to become killers.

Influenza viruses originate in wild waterfowl and have long spilled over and adapted to other species, including humans. There are three types. Type B and type C influenza viruses are human-adapted pathogens, which cause mild seasonal flu.

People were exposed to H5N1 through close contact with infected birds. Normal flu symptoms would turn into severe pneumonia, and for some, organ failure. More than half—59 percent—of those infected perished.50 And the virus spread.

Virologists call them the perfect “mixing vessel” for novel influenza strains.

By 2010, China was the world’s largest producer of pork, raising 660 million pigs, half of all the pigs raised in the world, and more than five times the production of countries such as the United States.

The crowds of pigs created what the virologist Michael Osterholm called “airborne clouds of virus” inside the barns, which were readily inhaled by local people.

The most nightmarish flu pandemic in modern times struck in 1918. The pandemic virus—H1N1—had amplified and grown virulent under the unusually crowded conditions of trench warfare during World War I.

It caused more than 40 million deaths around the globe, mostly due to bacterial pneumonia, a complication of the viral infection (which would be treatable today, unless caused by a resistant strain).

In a general sense, this happens when sufficient numbers of individuals choose to pursue their own private interests rather than public ones.

In 2002, Chinese authorities treated the emergence of SARS as an official state secret.

They blocked, at least initially, investigative teams from the WHO from inspecting the military hospitals where SARS patients were being treated.

Farmers profited by giving antibiotics to their livestock, which for reasons that are still unclear made them grow faster and helped them thrive in factory farms. (Their provision of low-dose antibiotics to their livestock for “growth promotion” accounts for 80 percent of all antibiotic consumption in the United States.)

In countries like India, where there are fewer restrictions on antibiotic consumption, overuse is rampant. Even the most high-end antibiotics are available without a prescription.

The poor, who can’t afford full courses of the drugs, pop one or two tablets at a time,

MRSA is rare in Finland, Norway, and Denmark, as well as the Netherlands, even in hospitals.

In 1977, the FDA proposed removing the antibiotics penicillin and tetracycline from use in livestock for growth promotion, but Congress blocked the move. Then in 2002, the FDA announced that it would regulate the use of antibiotics in livestock only if the practice could be proved to cause high levels of drug-resistant infections in people.

Nineteenth-century treatments for cholera increased its death toll from 50 to 70 percent.22 Since they considered cholera patients’ vomiting and diarrhea therapeutic, doctors treated patients with compounds that intensified the very symptoms that were killing them.