Crossing the divide: How Covid-19 and other deadly disease made the leap from animals to humans

Crossing the divide: How Covid-19 and other deadly disease made the leap from animals to humans

What do Covid-19, Ebola, Lyme and AIDS have in common? They jumped to humans from animals after we started destroying habitats and ruining ecosystems, writes Ferris Jabr

Crossing the divide: How Covid-19 and other deadly disease made the leap from animals to humans

IT MIGHT have started like this: One afternoon last year, somewhere in China’s mountainous Yunnan province, a hunter entered a limestone cave.

As he stepped carefully along the slick and uneven surface, his headlamp illuminated ruffled curtains of stone and walls popcorned with kernels of calcite. He continued through a series of smaller chambers until he reached a narrow passageway that reeked of ammonia. He stretched a fine-meshed net across the passage, sat down in a relatively dry area and waited.

As dusk fell, thousands of horseshoe bats — small and agile with baroquely furrowed noses — began streaming from the cave to hunt for insects.

There were so many flying so close together that some of them could not avoid the net. Once a majority of the bats were gone, the hunter untangled the dozen or so he caught, dropped them into a cloth sack and collected some fresh guano from the cave floor.

The next morning he took most of the bats to vendors at a nearby wildlife market, where they were stored in cages alongside peacocks, bullfrogs, rat snakes, soft-shell turtles, mouse-deer, ferret badgers and foxes, all being sold for their meat, fur or their supposed medicinal properties.

After selling the guano to farmers to be used as fertiliser, he took a few of the plumpest bats to restaurants he had been personally supplying for years.

Although he didn’t realise it, the hunter had caught much more than his quarry. Like all animals, the bats were planets unto themselves, teeming with invisible ecosystems of fungi, bacteria and viruses.

Through chance mutations and the frequent exchange of genes, one virus had acquired the ability to infect the cells of certain other mammals in addition to bats, should the opportunity ever arise.

When the hunter entered the limestone cave, he provided the virus with a new path to follow, one that led out of the damp crevices it had always known, out of the countryside, into the world at large.

Perhaps the hunter was contaminated by guano in the cave, transferring the virus to his nose or mouth with an absent-minded gesture. Maybe a market vendor or cook was infected by a splatter of blood or faeces when a bat was skinned and gutted.

As the many stressed and injured animals in the market bled, drooled and defecated on one another, the virus might have initially jumped from bats to another caged creature, such as a pangolin, hybridising with that animal’s viruses before leaping again to humans.

Crossing the divide: How Covid-19 and other deadly disease made the leap from animals to humans
A worker from China Biodiversity Conservation and Green Development Foundation, or CBCGDF, holds the Pangolin named Lijin before its release from the Jinhua wild animal rescue center in eastern China's Zhejiang province. (CBCGDF via AP)

When the chefs, traditional healers and other buyers browsed the market, they may have inhaled infectious droplets or touched contaminated surfaces, starting new chains of infection throughout the region.

At first, the virus might have proliferated at a rate sufficient to sustain itself, but not high enough to create noticeable clusters of infection. Eventually, through pathways of contagion linked to the trade and consumption of wildlife, the virus journeyed from villages in rural China to the city of Wuhan.

Soon it was moving rapidly from person to person in restaurants, offices, apartment complexes, hotels and hospitals. At some point in late 2019 or early 2020, the virus discovered a new way to travel: It boarded a 747.

There is much we don’t know about the origins of the ongoing pandemic and some details we may never learn. Though genetic sequencing currently indicates that horseshoe bats are the ultimate source of SARS-CoV-2, it’s possible another animal will eventually prove to be the vector.

Bats may have initially infected livestock or more exotic captive creatures raised on one of China’s many wildlife farms. Or maybe the virus was intermittently infecting animals and people in rural areas for years before finally finding a route to a major city. Regardless of SARS-CoV-2’s precise trajectory, experts agree that Covid-19 is a zoonosis, a disease that jumped from animals to humans. Between 60% and 75% of emerging infectious diseases in humans come from other animals. Many zoonoses — rabies, Lyme, anthrax, mad cow disease, SARS, Ebola, West Nile, Zika — loom large in public consciousness; others are less familiar: Q fever, orf, Rift Valley fever, Kyasanur Forest disease.

More than a few, including influenza, AIDS and the bubonic plague, have caused some of the deadliest outbreaks in recorded history. Although zoonoses are ancient, thought to be referenced in Mesopotamian tablets and the Bible, their numbers have increased in the last few decades, along with the frequency of outbreaks.

Zoonotic pathogens do not typically seek us out nor do they stumble onto us by pure coincidence. When diseases move from animals to humans, and vice versa, it is usually because we have reconfigured our shared ecosystems in ways that make the transition much more likely.

Deforestation, mining, intensive agriculture and urban sprawl destroy natural habitats, forcing wild creatures to venture into human communities. Excessive hunting, trade and consumption of wildlife significantly increase the probability of cross-species infection. Modern transportation can disperse dangerous microbes across the world in a matter of hours.

Even in Yunnan, one of China’s most rural and biodiverse provinces, rapid urbanisation has markedly disturbed local ecosystems. Logging and human-set fires have destroyed hundreds of thousands of acres of wilderness.

Houses, fruit trees and rubber plantations have displaced tropical rainforest. In 2015, an international team of scientists collected blood samples from 218 villagers in Yunnan who lived within four miles of bat caves.

Six villagers had antibodies for SARS-CoV-1, the virus that caused the original SARS outbreak in the early 2000s. None of the six individuals had a known history of SARS or contact with SARS patients but all had observed bats flying through their villages, suggesting the possibility of direct infection. Some scientists think such exposure is routine in the province.

Infectious-diseases experts have a term for the species in which a pathogen typically resides without causing serious illness: natural reservoir. We have linked the reservoirs of unfamiliar pathogens to our own through vast networks of accidental tributaries.

We plunge our nets into the native pools of exotic creatures and fling what we catch into once impossible congregations, allowing their microbes to mingle and mutate. We fill our hinterlands with artificial oceans of pigs and poultry, which become mixing vessels for viruses from humans, livestock and wildlife.

We drain the world’s biological basins of the diversity that would ordinarily keep contagions in check. Other animals’ diseases have not so much leapt onto us as flowed into us through channels we supplied.

While renewed attention to the hazards of wildlife markets is thoroughly warranted, many pathways of contagion between animals and people are not nearly so bloody or explicit.

Crossing the divide: How Covid-19 and other deadly disease made the leap from animals to humans
Experts agree that Covid-19 is a zoonosis, a disease that jumped from animals to humans which could originate in bats in cave, and below, like Lyme disease from a tick. -Photo by HECTOR RETAMAL/AFP via Getty Images-

In the Autumn of 1998, pig farmers in Malaysia began to develop a severe illness characterised by fevers, confusion and convulsions. Some slipped into comas.

Between September and May, the outbreak infected 265 people and killed 105, a fatality rate of nearly 40%.

Initially, many experts suspected Japanese encephalitis. In early 1999, however, Kaw Bing Chua, then a virologist in training at the University of Malaya, carefully stowed samples of the pathogen in his carry-on luggage and flew to a branch of the US Centres for Disease Control to use its powerful electron microscope.

Under high magnification, he could see that it was not the Japanese encephalitis virus. It did not seem to be an exact match for any known pathogen. Chua and his colleagues named the novel virus Nipah after the village where the samples originated.

Later in 1999, Chua began searching for Nipah’s natural reservoir. Earlier research by the epidemiologist Hume Field revealed that fruit bats were the reservoir for the related Hendra virus in Australia, so Chua’s team in Malaysia focused on bats as well.

They spread plastic sheets beneath roosting sites to collect dribbles of urine and bits of bat-nibbled fruit, such as mangos and waxy pink jambu air, also known as water apples. Live virus isolated from the samples closely matched the strains that caused the outbreak, confirming that fruit bats were the reservoir.

Rabies, Ebola, Marburg, SARS, MERS, Hendra, Nipah: Bats are a definitive or probable source of many of the most lethal zoonotic viruses to enter human populations.

Why? There are many reasons. Bats are an ancient and diverse lineage: Nearly one in four mammal species is a bat; as a group, they have been co-evolving with a vast array of viruses for around 50m years.

Many bat species are social: They roost in large numbers, huddle together for warmth, groom one another and suckle their young, providing numerous opportunities to circulate pathogens among themselves.

Bats also have a unique immune system, most likely as an adaptation to a talent no other mammal can claim. In order to fly, bats must significantly increase their metabolic rate, which creates dangerous molecular byproducts, such as reactive ions that damage cells and DNA.

During flight, bits of fractured DNA escape the nuclei of bat cells and drift about, resembling the presence of viral invaders.

In most animals, all that havoc and misplaced DNA would provoke a robust immune response and chronic inflammation, needlessly harming healthy tissue. As a result of these pressures, bats have evolved several countermeasures, including tempered inflammatory reactions.

In turn, these adaptations have made them more resilient to actual viruses and less likely to initiate the kind of overzealous immune response that often kills other infected animals.

Crossing the divide: How Covid-19 and other deadly disease made the leap from animals to humans
Commuters wear face masks to protect against the new coronavirus as they walk through a subway station in Beijing, Tuesday, June 23, 2020. -AP Photo/Mark Schiefelbein-

OUTBREAKS of bat viruses usually begin when a human takes a bat somewhere it would never go on its own or intrudes on its home. Nipah is a prime example. From the summer of 1997 to the summer of 1998, human-set fires in Southeast Asia incinerated at least five million hectares of drought-stricken forest.

With much of their native habitat logged or in ashes, and wild fruit trees less productive than usual, bats began feeding in orchards that bordered on forest.

When the virologist Kaw Bing Chua and his colleagues examined the farms in the area where the first cases occurred, they discovered mango, durian and jambu air trees adjacent to or overhanging pig enclosures.

As they foraged among the farms’ trees, saliva-soaked pieces of fruit would have fallen into the pigsties, providing the pigs with irresistible morsels and repeated doses of the virus. Farmers in close contact with infected pigs subsequently contracted the virus.

If this scenario sounds at all familiar, it’s probably because it inspired the closing scenes of the 2011 film

“Contagion.” Few people have willingly spent as much time inspecting ticks as the ecologists Felicia Keesing and Richard Ostfeld.

Longstanding scientific collaborators, who also happen to be married, they routinely catch and examine woodland mammals in the Hudson Valley.

With deft movements honed by decades of practice, they remove their quarry from their traps. If it’s a smaller animal — say, a mouse — they hold it by the scruff of its neck and count anywhere from 20 to 200 poppyseed-size ticks on its face and ears, gently parting its fur with their breath to get a better look. -For now, during the pandemic, they use tweezers instead.-

In more than two decades of research, Ostfeld and Keesing have discovered that the abundance of certain forest mammals predicts the size of tick populations the following year and the risk of Lyme disease for people who live nearby.

When larval ticks hatch, they do not yet carry the corkscrew-shaped Borrelia bacteria that cause Lyme; they acquire the pathogens from the wide array of small creatures on which they feed. For reasons of physiology and behavior, the probability that one of these animals will transmit Borrelia to a tick varies immensely.

Some species seem to have especially strong immune reactions to ticks, killing them before they can finish feasting. Others thwart parasites with fastidious grooming: An opossum might dispose of more than 5,000 ticks in a single week, while a mouse removes only 50. White-footed mice are by far the most tolerant of ticks and the most likely to spread Borrelia bacteria, infecting about 90% of ticks that feed on them. Wherever white-footed mice multiply, so does the threat of Lyme disease.

Crossing the divide: How Covid-19 and other deadly disease made the leap from animals to humans
White-footed mice are by far the most tolerant of ticks so wherever white-footed mice multiply, so does the threat of Lyme disease. Picture: Dr William J Weber

White-footed mice are what biologists call a generalist species: They are resilient, omnivorous and adaptable and, unlike more specialised species, they are capable of thriving in cramped and degraded habitats.

Expanding human populations are fracturing forest into increasingly tiny islands of green throughout the Northeast. The average patch of contiguous forest throughout much of the Hudson Valley is now a mere 182 acres.

In fragmented wilderness, where many creatures cannot survive and species diversity is low, white-footed mice populations boom and infect huge numbers of ticks with the bacteria that cause Lyme, escalating the risk to humans. Conversely, in high-diversity areas, populations of white-footed mice are constrained by numerous competitors and predators, most of which are far less likely to infect ticks with Borrelia, mitigating the risk of spillover, a phenomenon known as the dilution effect.

Since the 1990s, when Ostfeld and Keesing began their studies, researchers working in many different ecosystems have discovered that high biodiversity often dampens the risk of infectious disease.

“The best hosts for many diseases are often the very species that thrive when humans disturb habitats and diversity declines,” Keesing said. “Eventually we realised that what we thought was a peculiarity of the Lyme disease system was happening all over the planet.”

Eliminating zoonoses is effectively impossible. But we can significantly reduce the risk of dangerous pathogens spilling from animals into human populations. In the wake of SARS and the early stages of Covid-19, the most obvious target for reform is the wildlife trade.

In some cases, people depend on wildlife for sustenance. Some 150m households in Latin America, Asia and Africa hunt wild animals, primarily for personal consumption, according to a 2017 estimate; poorer households tend to rely most strongly on wild meat.

According to another 2017 study, meat consumption in China has increased by a third since 2000, more rapidly than in any other major economy, and demand for wildlife products of all kinds has surged.

In the US, 11.5m people hunt and sometimes eat animals such as deer, elk, moose, bears, raccoons, porcupines, doves, quail, pheasants, armadillos, squirrels and alligators.

Crossing the divide: How Covid-19 and other deadly disease made the leap from animals to humans
Lyme Disease infected tick.

ALL-ENCOMPASSING bans are not necessarily the most realistic or judicious strategy. Stricter regulation, improved hygiene and embargoes on wild creatures that pose the greatest zoonotic risk — bats, rodents and primates — could make live-animal markets substantially safer.

Some researchers advocate for solutions that address underlying socioeconomic issues: developing alternative sources of income for hunters and animal traders, investing in food security and promoting protein-rich plant crops.

Many of the other major drivers of zoonoses are the same intractable problems that conservationists have been grappling with for decades: deforestation, loss of biodiversity, depletion of natural resources. Yet even relatively simple changes to the interfaces between humans and other animals can have big effects on the probability of a spillover.

Following the 1998 outbreak of the Nipah virus in Malaysia, pig farming was prohibited in high-risk areas; farmers separated pig sties and fruit trees, kept pigs in smaller groups isolated from people and other animals and started using more protective gear and disinfectants. So far the disease has not resurfaced in Malaysia.

Ultimately, the prevention of zoonoses demands more than practical interventions; it requires a fundamental shift in perspective. Humans have a long history of treating the world as our stage and other creatures as our props.

More than any other entity, viruses and microorganisms expose the fallacy of our tyrannical choreography. We are used to thinking of ourselves as the protagonists of every landscape, but from the perspective of infectious microbes, we and other large creatures are the landscape.

As we restructure Earth’s biosphere to suit our whims, we open hidden conduits between other animals’ microbiomes and our own. Once those channels are in place, pathogens can no more stop themselves from spilling into us than water can prevent itself from running downhill.

We cannot blame the bats, mosquitoes and viruses. We cannot expect them to go against their nature. The challenge before us is how best to govern ourselves and stymie the flood we unleashed.

Adapted from an article that originally appeared in The New York Times Magazine.

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