Deep in the Amazon, scientists race against time to identify unknown pathogens

A University of Brasilia bat researcher holds a bat captured for research in Brasilia, Brazil, 28 June 2021.

The next deadly virus that spreads around the world could easily come from a bat that roosts in or around the caves being explored by Thiago Bernardi Vieira.

Vieira, a biologist from Brazil's Federal University of Para, is the recipient of research grants including one titled "The Least Known Bat Species in Brazil." His mission: to collect basic information about bats here in the Amazon rainforest.

He has his work cut out for him.

Just how big a chore he faces was easy to see during a July 2021 foray to the giant Planaltina cavern, where he sought to catch samples of the many species believed to be living there. Vieira trained his headlamp on a bat with a long, sharp nose.

"I've never caught one of these here before," the scientist said, untangling the animal gently from a net he'd spread across the cave's mouth.

In the depths of the world's largest rainforest, what science knows about wildlife is as limited as the jungle is vast. Beyond Planaltina, one of the better-known caves in the Amazon, countless other habitats – and bat species native to them – remain completely unstudied or undiscovered. And with limited funding available to researchers, scientists don't expect to unravel the Amazon's mysteries anytime soon.

"We don't know anything," said Vieira, whose shoestring budget for his "least known species" project totaled about $3,000. He recently won a second grant, totaling just over $21,000, to continue his research.

Some of the most devastating viruses that have infected humans over the past century have emerged from bats. For reasons including their sheer number and diversity, the animals are a significant reservoir of pathogens that can sicken people. And because of the vast size of the Amazon rainforest, and rapid human encroachment into its little-known habitats, some scientists see Brazil as a likely cradle of a future pandemic.

"The potential for new viruses is huge," said Erika Hingst-Zaher, a zoologist at the Instituto Butantan, a prominent research facility in Sao Paulo, and a member of PREVIR, a nationwide network of scientists documenting pathogens carried by bats and other animals. "People are betting the next pandemic will come from Brazil."

Brazil's health ministry, in a statement to Reuters, said there is no evidence at present that the risk of a new virus emerging from wildlife represents "a public health emergency of national importance."

Home to the third-highest number of bat species on the planet by one authoritative count, Brazil has seen its chances of birthing an unknown virus soar as people increasingly clear rainforest to make way for logging camps, mines, ranches and settlements.

If a never-before-seen pathogen – one even more contagious than the one that causes COVID-19 – were to escape the Brazilian Amazon, a Reuters simulation shows, it could infect 1.2 billion people within six months. That's exponentially more people than the 10.5 million who caught COVID-19 in the pandemic's first six months.

Brazil has more areas of high risk than any other country, Reuters found – 1.5 million sq km of land with prime conditions for zoonotic spillover, as leaps by viruses from animals into humans are known.

For its analysis, Reuters examined environmental conditions around 95 locations worldwide where bat viruses infected humans between 2002 and 2020. The news agency then used a computer model to estimate where similar conditions existed globally for each year during the period and identified areas most prone to spillover – dubbed "jump zones."

In Brazil, the analysis identified risky locales covering a combined area roughly three times the size of France. Driven by conditions including deforestation and other incursions by humans on bat habitats, these Brazilian jump zones have grown by more than 40 per cent in extent over the past two decades – over 2.5 times faster than similarly risky areas worldwide, Reuters found.

Almost three-quarters of Brazil's jump zones lie within the Amazon, a tangle of biodiversity that holds more secrets than scientists can ever hope to discover, especially with swaths of the rainforest quickly succumbing to development. With each new incursion into the jungle, the opportunity increases for a new and deadly pathogen to spill over, proliferate locally, and potentially spread to the rest of Brazil and the world.

Brazil is unprepared for such an event.

The country's health system and scientific research institutions, scientists and health experts warn, are underfunded and ill-equipped to spot a dangerous pathogen, whether novel – like the one modeled by Reuters – or known, such as those that cause SARS and Nipah.

Both of those lethal illnesses at first resemble the flu or the common cold in their victims. The similarity to routine ailments can allow a deadly new virus to transmit silently and evade surveillance, at least initially.

"If you're not looking for a novel virus, you're not seeing it," said Ana Pastore y Piontti, a Boston-based data scientist who specializes in epidemiology and co-authored the 2018 book "Charting the Next Pandemic."

In a rainforest larger than Western Europe, many communities, especially those at the frontiers of deforestation, lack hospitals. The nearest medical facilities are often hours or days away by boat or road.

During the pandemic, hundreds of Indigenous people died without reaching hospitals. And the sick that made it to Amazon cities like Manaus and Altamira found long waits for hospital beds and an overwhelmed medical system in collapse.

"The healthcare system was not ready for coronavirus," said Marcelo Salazar, who until recently was the Brazil coordinator for Health in Harmony, an organization that focuses on health and the environment. "Obviously it's not ready for future pandemics."

In its statement, the Health Ministry said it monitors the risk of zoonotic spillover daily through several networks and programs, including 815 epidemiological centers in hospitals around the country. Those centers, it added, are specifically tasked with identifying emerging illnesses.

The ministry said it is also studying the creation of a working group to improve zoonotic surveillance that would include representatives of the agriculture, environment, academic and health sectors.

The pathogen's path

One major route by which humans could carry such a virus out of Brazil's rainforest, according to the Reuters data analysis, is also a major driver of spillover risk there: the Transamazonian Highway.

Eager to improve upon a history of disorganized, impermanent settlement, Brazil's government authorized construction of the road in 1970. In various states of construction and disrepair ever since, it cuts east-west through the Amazon, its more than 4,000 km a backbone for further inroads into the jungle.

Those inroads are at the heart of spillover risk, the Reuters analysis found, because they create yet more areas of possible interaction between humans and potentially dangerous viruses. Though the news agency's computer model accounts for only some of the risk factors contributing to disease outbreaks, one conclusion is clear: Deforestation and human intrusion on bat habitats consistently drive up risk and often precede spillover.

Some scientific studies have found that deforestation causes stress in bats, and stressed bats carry more viruses and shed more germs in their saliva, urine and feces.

Deforestation is hardly new in the Amazon.

People have sought to develop the rainforest since the early days of Brazil's colonization – from 17th-century explorers sent by the Portuguese crown in search of silver to the rubber barons who milked the region in the 19th century to provide latex for industry. More recently, development has centered on agriculture and the potential, with the Amazon's mighty rivers, for hydroelectric power.

Deforestation has ebbed and flowed over the decades.

It spiked following the highway's construction, making the Amazon in the early 1980s a rallying cry for the global environmental movement. Since the turn of this century, deforestation within 30 km of the highway has exceeded 30,000 sq km, an area the size of Belgium.

Under the recent administration of President Jair Bolsonaro, a far-right populist, destruction across the region soared. His administration rolled back environmental regulations, slashed funding for scientific research, scoffed at the threat of COVID-19, and received scorn at home and abroad for a slow, dismissive response to the pandemic.

Bolsonaro left the presidency in January. A lawyer for Bolsonaro said the former president declined to comment on his role in accelerating deforestation.

Satellites detected more than 25,000 sq km of new tree loss across the Amazon in 2020. The combined clearings totaled more than 400 times the area of Manhattan.

The destruction, according to a Reuters analysis of data compiled by a University of Maryland-led team of researchers, was the most since 2016 and 2017, when rampant wildfires drove massive tree loss. And the rapid losses continue: Brazil's space research agency, using satellite data, said in November that deforestation fell slightly in 2022 but remained near a 15-year high.

President Luiz Inacio Lula da Silva, Bolsonaro's successor, successfully slowed destruction during a previous term as president starting in 2003. At the time, his administration improved law enforcement in the rainforest and blocked access to credit for ranchers and others caught illegally clearing woodland.

He has said he will eliminate deforestation in Brazil by 2030 and has boosted the budget for environmental enforcement, made it easier to collect fines against those who clear land illegally, and set up a task force to investigate fraud in the lumber trade.

Despite the new president's lofty goals, he would need to revamp Brazilian law to fully eliminate deforestation. Some destruction is legal at present, especially for agricultural purposes, and powerful legislators allied with Brazil's farm lobby are unlikely to make his efforts easy.

Elected officials from opposition parties, and lawmakers from farming regions, have already said they will oppose any effort to change the existing "forest code," as Brazil's woodland legislation is known. "Brazil's enemy is illegal deforestation, not deforestation permitted in the forest code," said Jose Vitor de Resende Aguiar, a Congressman from Bolsonaro's party and a representative of the farm caucus.

The steady pace of destruction, even before Bolsonaro, has been such that scientists say it is only a question of time before a spillover happens. "We raise a red flag for the current risks of ZD emergence in Brazil," wrote a group of researchers, abbreviating zoonotic disease, in a 2022 study published by Science Advances, a scientific journal.

"We have very little data"

So far, Brazil – and humanity – have been lucky to avoid a major spillover from the Amazon, researchers say. Chances of a novel virus emerging from the region are high.

When examining spillover risk, scientists use the number of bat species in a given area as a key variable.

One reason is that bats' physiology is similar enough to other mammals, including humans, to provide a reasonable chance that some of the viruses they host could thrive in those species, too. And because bats live in close quarters, regularly dousing each other with bodily fluids, their pathogens easily spread, evolve and mutate, sometimes becoming more virulent and transmissible.

When humans encroach on their habitat, and bat species commingle, the viral cocktail intensifies. "There's kind of more of a melting pot," said Rory Gibb, a biologist at University College London. "Closer contact with people means there is always potential for some of those viruses to be problematic."

With 172 documented species – and likely many more yet to be identified – Brazil has the third-greatest variety of bats in the world, following Colombia and Indonesia, according to data compiled by the International Union for Conservation of Nature and Natural Resources.

Ludmilla Aguiar, a biologist at the University of Brasilia, said so little is known about bats in the rainforest that it could take hundreds of years, given the current state of research and funding, for scientists to document even elementary information about all the possible species and habitats specific to them.

Researchers have already identified some viruses in Brazilian bats that are known to infect humans. They include rabies, which occasionally causes outbreaks, particularly as cattle farms eat into the forest and provide an ever-expanding food source for vampire bats.

Brazilian bats have also been shown to carry coronaviruses and hantaviruses, deadly pathogens commonly associated with rodents that can cause hemorrhagic fever and lung infections.

What worries some scientists most, though, are the viruses they don't know.

"We have very little data to really discuss their pathogenicity," biologist Aguiar said, using a term describing the ability of a germ to cause disease.

Although no major spillover from Brazilian bats has been reported to date, researchers don't rule out unrecorded leaps by unknown pathogens in the past. A novel virus may have swept through native tribes or remote villages at some point, but died out before it spread elsewhere.

"Odds of it being documented are very slim," said Caio Graco Zeppelini, an ecologist and bat researcher at the Federal University of Bahia.

A race against time

One July evening, Vieira, the bat-catching biologist, gathered with a group of students outside Planaltina. The cave, a web of caverns extending more than 1.5 km underground, is home to thousands of bats. Many more caves like it exist throughout the Amazon.

Darkness fell. The screech of bats intensified as the animals flew out to forage.

Professor and students draped nets outside the gaping entrance to the caverns, eager to see what species they might capture. Within 40 minutes, they had trapped about 200 bats, including the Tomes' sword-nosed bat, the animal with the long, sharp snout Vieira had previously only seen elsewhere.

Another specimen in the nets: a small, mustachioed bat that scientists in 2018 identified as a new species. The bat, Pteronotus alitonus, is still being studied by biologists. Many other bats are even less understood.

"We don't know what they eat, where they live, what type of shelter they prefer," Vieira said.

His roughly $3,000 grant for the project was awarded by the Brazilian Bat Research Society, a nationwide organization of scientists. A more recent and bigger grant he received will help him continue exploring area caves. The grant was financed by Brazilian mining giant Vale SA VALE3.SA, as part of a deal with the government to offset the environmental impact of one of its iron ore mines, also in Para state.

Vale, in an emailed statement to Reuters, said it finances such research on its own and also through agreements with the government. As part of the same agreement funding Vieira's research, it has awarded a total of about $1.58 million in grants for 30 projects, including six related to bat studies.

While his grants have been modest, the funds help Vieira cover some of his costs as he catalogs species within a 300 km radius around Altamira, a fast-growing city of 135,000 people on the nearby Xingu River, a major tributary of the Amazon.

From Altamira, he drives his tiny hatchback for hours on rough roads and makes arduous hikes into the jungle, toting heavy equipment in punishing heat. He also contends with rapidly changing landscape; rainforest he surveys sometimes gets cleared for farmland seemingly overnight.

Planaltina itself is now a small island of forest surrounded by cow pastures. Even here, by the cave's mouth, a property owner has poured concrete over a stream flowing naturally from the cave, diverting the water into an artificial pool. Locals pay about $3 on the weekend to swim, chill by the pool, and drink beer – just meters from where the bats swarm as they enter and exit the cavern.

"It's a pretty spot," Vieira said. "It's not exactly natural anymore."

Other Brazilian scientists are also hard at work elsewhere in the field and in labs across the country. Researchers associated with PREVIR, a nationwide network that is documenting bats and other animals and the viruses they carry, are gathering data from specimens in the Amazon and other biomes across Brazil – Atlantic rainforest, Pantanal wetlands, tropical Cerrado savanna, Pampas grasslands, and coastal habitats.

Since its launch in 2020, PREVIR has received funding worth roughly $2.3 million from Brazil's government, enough to accomplish a set list of goals but far less than scientists in the country say is necessary to gain a broad understanding of risk in the Amazon. And funding for science as a whole has plummeted in Brazil since the country endured a two-year recession last decade and sluggish growth most years since.

Lula has pledged to rebuild state support for the sciences.

The PREVIR scientists, a total of nearly 50 researchers from 16 institutions, wear thick gloves, protective glasses and other gear to protect against bat bites and contamination. They record field data on a smartphone app made for the network and then upload it to a database. Bat blood samples are sent to the laboratories for screening and genetic sequencing.

If a novel virus with spillover potential is discovered, the team will work toward developing a vaccine, said Helena Lage Ferreira, a virologist at the University of Sao Paulo and a coordinator of the network.

Scientists worry that some species may disappear before they can learn enough about them. Of particular interest, since bats rarely succumb to viruses, is studying any immunity they carry.

"Somehow they developed adaptations to deal with those viruses," said Enrico Bernard, a conservation biologist at the Federal University of Pernambuco and the president of the Brazilian Bat Research Society. "It may be in the immune systems of bats lie the secrets of how to deal with pandemics in the near future."