Pandemic: Tracking Contagions, from Cholera to Coronaviruses and Beyond

by Sonia Shah

Muslims must perform ablutions at least three times before their five-times-daily prayers, as well as on numerous other occasions.

Prominent Christians openly repudiated water’s cleansing effect as superficial, vain, and decadent. “A clean body and a clean dress,” opined one, “means an unclean soul.” The most holy Christians, with their lice-infested hair shirts, were among the least washed people on Earth.

Leaders of Christian Europe, like political leaders everywhere facing an incomprehensible threat, blamed their favorite bugbear, water-based hygiene. In

“Water was the enemy,” writes the hygiene historian Katherine Ashenburg, “to be avoided at all costs.”

According to a history of sanitation by the journalist Rose George, the sixteenth-century German monk Martin Luther ate a spoonful of his own feces every day.

The Dutch built their privies to open at ground level and pour their contents into the streets, so that “hogs may consume the filth and wallow in it,” as a New Amsterdam official put it in 1658. The English, who took control of the colony in 1664 and renamed it “New York,” similarly contained their excreta in what they called “ordure tubs,” which they, too, emptied into the streets.14

Of course, New Yorkers didn’t know that their polluted waters could transmit deadly diseases. But they did know that it tasted bad, so they rarely drank water straight. They turned it into beer or they added liquor, like gin,

The island, wrote George Washington in 1781, was “totally stripped of Trees, & wood of every kind.” The only thing left was “low bushes.”

hills (inspiration for the Lenape name for the island, “Mannahatta,” or “Island of Many Hills”),

The worst flooding occurred in the many low-lying, sinking properties that had been “reclaimed” from the sea. The city had sold parcels of sea and pond called “water lots” to entrepreneurs, who displaced the water and constructed housing atop it. More than 130 acres of land around the coasts had been thus reclaimed, turning the once pointy tip of Manhattan into a rounded arc.32

In the United States, the mean size of hog farms grew by more than 2,000 percent between 1959 and 2007; the mean size of farms where chickens are raised for meat grew by over 30,000 percent.54

In 2011, a batch of fenugreek seeds in Egypt caused an outbreak of disease three thousand miles away in Germany. That outbreak was noteworthy for two reasons. It showed the long reach of fecal-contaminated products and how they pose a risk to everyone along the global food chain. It also showed how pathogens exploit fecally contaminated environments not only for their transmission opportunities but also to become more virulent.

Filth is just a symptom. The real problem is crowding.

The intensity of the epidemic led to its own collapse. By the end of the summer, cholera had rid the city of susceptible victims.

As a result of discriminatory English policies, Irish tenant farmers had only scarce, marginal lands with which to feed their families. The potato was the only crop they could afford.

As the potato crop wasted, famine set in. One and a half million perished. Another 1.5 million fled the Phythophthora-devastated countryside, their travel overseas subsidized by their own landlords, who preferred to facilitate their departure rather than contribute more to famine relief efforts, as the Irish government demanded.9

Between 1847 and 1851, nearly 850,000 refugees from Ireland landed in New York City.

New York’s doctors claimed they could spot basement dwellers by a glance at their pale faces and a sniff of their musty odor.

City officials were only dimly aware of the health hazard that Five Points posed to the rest of the city. At one point, they considered razing parts of the neighborhood to build a prison.

By 1850, in the slums of New York City, nearly two hundred thousand people crammed into each square mile. That’s nearly six times more crowded than modern-day Manhattan or central Tokyo, and over a thousand times more crowded than any group of humans had ever lived before.

After a seventeen-year absence, cholera returned to New York City in 1849 with a vengeance.

Unbeknownst to the rest of the city, 150 others scaled the warehouse walls, boarded small boats, and escaped into the metropolis.

Deaths outnumbered births. Despite the greater availability of food and paid work, children under the age of five who lived in cities died at nearly twice the rate as those living in the countryside.

Even those who survived suffered the price of urban living. Their poor health stunted their growth: the average height of West Point cadets born between 1820 and 1860, as the nation became more urbanized, declined by a half inch. The

In the years after the 1849 cholera epidemic in New York, immigrants continued to stream into the city, at the rate of nearly twenty-three thousand every month. They were more than enough to replace the parade of corpses flowing out of the city.23

His 1889 book How the Other Half Lives helped ignite a movement for tenement reform in New York City. One of the first reforms, the Tenement House Act of 1901, required that city buildings provide exterior windows, ventilation, indoor toilets, and fire protections.

A sliver of the old neighborhood became what is today Chinatown.

Passersby would never suspect that a riotous neighborhood of any kind once existed there.

in part to a lack of governance, housing regulations are as sparse and poorly enforced as in nineteenth-century New York.

By 2030, experts estimate, that will change. The majority of humankind will live in large cities.

because social contact continues even when infected people are dead.

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.

So long as mosquitoes keep biting, the pathogens continue to spread,

There are three types. Type B and type C influenza viruses are human-adapted pathogens, which cause mild seasonal flu. Type A are those viruses that have remained in their original reservoirs: ducks, geese, swans, gulls, terns, and waders.39

But the domesticated birds, unlike the wild ones, have no immunity to flu viruses. The pathogen replicates with abandon in their bodies, evolving new, more deadly strains called “highly pathogenic avian influenza” or HPAI.

40 The process is so reliable that scientists can reproduce it in the lab, creating more deadly strains of avian influenza simply by passing the virus repeatedly through chickens.41

As the virus’s basic reproductive number increased, so did the frequency and scale of the outbreaks it caused. Between 1959 and 1992, outbreaks of deadly avian influenza had occurred roughly every three years. Most affected fewer than five hundred thousand birds. Between 1993 and 2002, outbreaks occurred once every year, and between 2002 and 2006, they occurred every ten months. About half of these outbreaks affected millions of birds at a time.47

Of all the new pathogens emerging today, novel influenza viruses like H5N1 are the ones that keep the most virologists up at night.

Even with low mortality rates, seasonal flu viruses carry off huge numbers of victims, simply because they are so good at spreading widely among us.

So far, the virus has evolved into at least ten distinct lineages, or “clades,” all with varying abilities and proclivities.

After we landed, he held a vomit bag to his face, coughed up a wad of mucus, spit it out, and stuffed the bag back into the seat pocket.57

Precisely how H5N1 gained the ability to infect humans is not clear. Some experts speculate that another crowd of livestock—pigs—may have played a role.

One of the biological barriers to the spread of bird influenzas in humans is the fact that bird-adapted viruses bind to sialic acids in birds that are not present in humans. Theoretically, H5N1 or some other bird-adapted virus could spontaneously mutate in such a way that allows it to bind to human sialic acids.

reassortment. This is when a virus acquires a chunk of new genes from another virus, and with the newly acquired genes,

example one of the many influenza viruses already adapted to humans, such as the relatively mild ones that cause seasonal flu. Then the novel avian influenza virus could acquire the ability to transmit efficiently in humans,

Reassortment of this kind could happen only in cells coinfected with both viruses at the same time.

But since human influenzas bind to human sialic acids, and avian influenzas to avian sialic acids, people aren’t easily infected with bird influenzas, and birds ...

Pigs have both humanlike sialic acids on the surfaces of their cells as well as avian-like ones.

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

Whoever slept there inhaled the virus-laden air all night long.