In the summer of 2020, six months after the coronavirus pandemic, scientists traveled to the forests of northern Laos to capture bats that may harbor close cousins of the pathogen.
In the dead of night, they used mist nets and canvas traps to snag the animals as they emerged from nearby caves, collected saliva, urine, and feces, then released them back into the darkness.
The fecal samples were found to contain coronaviruses, which the scientists studied in high-security biosafety labs, known as BSL-3, using specialized protective gear and air filters.
Three of the Laos coronaviruses were unusual: They carried a molecular hook on their surface that was very similar to the hook on the virus that causes Covid-19, called SARS-CoV-2. Like SARS-CoV-2, their hook allowed them to cling to human cells.
“It’s even better than early strains of SARS-CoV-2,” said Marc Eloit, a virologist at the Pasteur Institute in Paris who led the study, referring to how well the hook on the Laos coronaviruses binds to human cells. The study was posted online last month and has not yet been published in a scientific journal.
Virus experts roar with the discovery. Some suspect that these SARS-CoV-2-like viruses may already be infecting humans from time to time, causing only mild and limited outbreaks. But under the right conditions, the pathogens could give rise to a Covid-19-like pandemic, they say.
The findings also have important implications for the charged debate about the origins of Covid, experts say. Some people have speculated that SARS-CoV-2’s impressive ability to infect human cells could not have evolved from an animal’s natural overflow. But the new findings seem to suggest otherwise.
“That really makes the notion that this virus had to have been invented or somehow engineered in a lab to infect humans so well,” said Michael Worobey, a University of Arizona virologist who was not involved in the work.
These bat viruses, along with more than a dozen others discovered in recent months in Laos, Cambodia, China and Thailand, could also help researchers better anticipate future pandemics. The viruses’ pedigrees offer hints as to where potentially dangerous strains lurk and which animals scientists should look to to find them.
Last week, the US government announced a $125 million project to identify thousands of wild viruses in Asia, Latin America and Africa to determine their risk of overflow. dr. Eloit predicted that many more relatives of SARS-CoV-2 could be found.
“I’m a fly fisherman,” he said. “If I can’t catch trout, it doesn’t mean there aren’t trout in the river.”
When SARS-CoV-2 first came to light, its closest known relative was a bat coronavirus that Chinese researchers found in 2016 in a mine in southern China’s Yunnan province. RaTG13, as it is known, shares 96 percent of its genome with SARS-CoV-2. Based on the mutations carried by each virus, scientists have estimated that RaTG13 and SARS-CoV-2 share a common ancestor that infected bats about 40 years ago.
Both viruses infect cells using a molecular hook called the “receptor binding domain” to attach to their surface. The hook of RaTG13, adapted for attachment to bat cells, can only weakly attach to human cells. The SARS-CoV-2 hook, on the other hand, can trap cells in the human airways, the first step towards a potentially fatal case of Covid-19.
To find other close relatives of SARS-CoV-2, wildlife experts checked their freezers full of ancient samples from around the world. They identified several similar coronaviruses from southern China, Cambodia and Thailand. Most came from bats, while a few came from scaly mammals known as pangolins. No one was a closer relative than RaTG13.
dr. Eloit and his colleagues instead set out to look for novel coronaviruses.
They traveled to northern Laos, about 240 miles from the mine where Chinese researchers had found RaTG13. In six months, they captured 645 bats belonging to 45 different species. The bats harbored two dozen types of coronaviruses, three of which were strikingly similar to SARS-CoV-2 — especially in the receptor-binding domain.
In RaTG13, 11 of the 17 major domain building blocks are identical to those of SARS-CoV-2. But in the three viruses from Laos, no fewer than 16 were identical – the best match yet.
dr. Eloit speculated that one or more of the coronaviruses could infect humans and cause mild illness. In a separate study, he and colleagues took blood samples from people in Laos who collect bat guano for a living. Although the Laotians showed no signs of being infected with SARS-CoV-2, they carried immune markers called antibodies that appeared to be caused by a similar virus.
Linfa Wang, a molecular virologist at Duke-NUS Medical School in Singapore who was not involved in the study, agreed that such an infection was possible because the newly discovered viruses can attach tightly to a protein on human cells called ACE2.
“If the receptor binding domain is ready to use ACE2, these guys are dangerous,” said Dr. Cheek.
Paradoxically, some other genes in the three Laotian viruses are more closely related to SARS-CoV-2 than other bat viruses. The cause of this genetic patchwork is the complex evolution of coronaviruses.
If a bat infected with one coronavirus catches a second, the two different viruses can end up in one cell at the same time. As that cell begins to replicate each of those viruses, their genes are shuffled, producing new virus hybrids.
In the Laotian coronaviruses, this gene shuffling has given them a receptor-binding domain very similar to that of SARS-CoV-2. The original genetic swap happened about a decade ago, according to a preliminary analysis by Spyros Lytras, a graduate student at the University of Glasgow in Scotland.
Mr. Lytras and his colleagues are now comparing SARS-CoV-2 not only with the new viruses from Laos, but also with other close relatives found in recent months. They find even more evidence of gene shifting. This process — known as recombination — can change the viruses from year to year.
“It’s becoming increasingly clear how important recombination is,” said Mr. Lytras.
He and his colleagues are now drawing the messy evolutionary trees of SARS-CoV-2-like viruses based on these new insights. Finding more viruses could help clear up the picture. But scientists are divided on where to look.
dr. Eloit believes the best bet is a zone in Southeast Asia that contains where his colleagues found their coronaviruses, as well as the nearby mine in Yunnan where RaTG13 was found.
“I think the main landscape corresponds to Northern Vietnam, Northern Laos and Southern China,” said Dr. eloit.
The US government’s new virus-hunting project, called DEEP VZN, may yield one or more SARS-CoV-2-like viruses in that region. A spokesperson for USAID, the agency funding the effort, named Vietnam one of the countries researchers will search for, saying novel coronaviruses are one of their top priorities.
Other scientists think it’s worth looking further afield for relatives of SARS-CoV-2. dr. Worobey of the University of Arizona said some bat coronaviruses with SARS-CoV-2-like segments have been found in eastern China and Thailand.
“Clearly, the recombination shows us that these viruses are part of a single gene pool over hundreds and hundreds of miles, if not thousands of miles,” said Dr. Worobey.
Colin Carlson, a biologist at Georgetown University, suspects that a virus that could trigger a Covid-like outbreak may be lurking even further. Bats, as far east as Indonesia and as far west as India, he noted, share many biological characteristics with the animals known to carry SARS-CoV-2-like viruses.
“This isn’t just a problem in Southeast Asia,” said Dr. Carlson. “These viruses are diverse and more cosmopolitan than we thought.”
Interest in the origins of the pandemic has drawn attention to the safety measures researchers use when studying potentially dangerous viruses. To win DEEP VZN grants, scientists must submit a biosafety and biosafety plan, including training for personnel, guidelines for protective equipment to be worn in the field, and safety precautions for laboratory work, according to a USAID spokesperson.
If scientists find more close cousins of SARS-CoV-2, it doesn’t necessarily mean they pose a deadly threat. They may not be able to spread in humans or, as some scientists speculate, cause only minor outbreaks. Only seven coronaviruses are known to have crossed the species barrier to become established human pathogens.
“There’s probably a lot of other coronaviruses that end up going nowhere,” said Jessica Metcalf, an evolutionary ecologist at Princeton University.
Still, recombination could potentially turn a virus that isn’t going anywhere into a new threat. In May, researchers reported that two canine coronaviruses have recombined in Indonesia. The result was a hybrid that infected eight children.
“If a coronavirus that we’ve been eyeing for decades that we think is something our pets can get can make the leap – we should have seen that coming, right?” said Dr. Carlson.