Bat virus studies raise questions about lab tinkering

In mid-2020, a team of scientists catching bats in Lao caves discovered coronaviruses strikingly similar to those that had started wreaking havoc around the world.

In the months since, some of these researchers have been studying one of these mysterious bat viruses at a high-security laboratory in Paris, hoping to find clues as to how its cousin SARS-CoV-2 became a global threat that has killed an estimated 15 million people.

Her work was scientifically fruitful. Last year, the scientists discovered that the bat virus can attach itself to human cells, at least in petri dishes. Last month, the team reported more reassuring news: that the virus is not particularly harmful to laboratory animals. The finding suggests that SARS-CoV-2 evolved its ability to spread rapidly and cause deadly disease only after the two lineages split from each other in the viral evolutionary tree.

If the Laotian virus ever jumps from a bat to a person, it could cause mild stomach upset rather than life-threatening pneumonia, according to new research. Still, lab experiments like these spark a long-standing debate among scientists about the wisdom of tinkering with viruses so closely related to a known pathogen.

Proponents argue that this type of data is critical to understanding – and preventing – pandemics. For example, the new studies tested whether bat viruses could evolve a “furin cleavage site,” a property of SARS-CoV-2 that allows it to efficiently infect human cells.

“Our motivation was to try and provide some insight into the origin of Covid,” said Marc Eloit, a virologist at the Pasteur Institute in Paris who is leading the effort.

But critics say that given the small but real chance that these engineered pathogens could infect lab workers and escape into the outside world, scientists shouldn’t conduct experiments that could improve the spread of viruses among humans.

“For me, the benefits of this work outweigh the risks,” said Dr. David Relman, microbiologist at Stanford University.

The bat virus, which is at the center of Dr. Eloit’s experiments was brought to light during an expedition to limestone caves in northern Laos in the summer of 2020. A team of Lao and French researchers caught bats flying out of the caves and took samples of their saliva. blood, urine and feces.

The scientists found genetic material from five coronaviruses that are closely related to SARS-CoV-2. In the droppings of a Marshall horseshoe bat, they found whole viruses of a strain they named BANAL-236 (a code indicating the virus came from a bat anal swab).

Back in their lab, the scientists determined that BANAL-236 can infect human cells by tightly binding to the same protein that SARS-CoV-2 uses to gain entry. The researchers published these results in the journal Nature in February.

Last month they released a second wave of results, now being reviewed by a scientific journal, in which they examined the virus’ behavior in laboratory mice and monkeys.

In one experiment, scientists injected the virus into genetically engineered mice, which are commonly used to study Covid. SARS-CoV-2 replicates rapidly in their lungs, just like it does in humans, causing them to lose weight and die.

BANAL-236, on the other hand, struggled to get lodged in the animals’ lungs and produced only about 1 percent of the viruses produced during SARS-CoV-2 infection.

The researchers found that the virus was even milder when they sprayed it up the noses of two monkeys. BANAL-236 replicated primarily in their intestines and not in their lungs.

dr Eloit suspects BANAL-236 is milder because it lacks a key trait important for SARS-CoV-2 success.

After a new SARS-CoV-2 virus is created in a cell, its spike protein changes shape, with an effect like the cocking of a crossbow. Then, when the virus binds to a new cell, the primed spike protein shoots out molecular bolts that pull it into its new host.

This shape-changing region of the tip – known as the furin cleavage site – is critical to the success of SARS-CoV-2. When scientists have engineered viruses that lack this site, the mutants have trouble replicating in the lungs of laboratory animals or spreading to new hosts.

Obtaining a furin cleavage site may have been a crucial step in the development of SARS-CoV-2. To explore this possibility, Dr. Eloit and his colleagues conducted laboratory experiments to enable BANAL-236 to develop new properties, such as B. a furin cleavage site.

The team based their studies on experiments in which other scientists had injected bird flu viruses into chicken eggs and waited for them to replicate. Then they transferred the new viruses into new eggs and allowed them to replicate again. With each transfer, the virus had a chance to evolve. After 11 transmissions, the scientists found that the flu viruses had evolved cleavage sites that made them more deadly to chickens.

Similarly, the Pasteur researchers removed lung tissue from mice infected with BANAL-236 and used the tissue to infect healthy animals. Then they repeated the cycle, transmitting virus from mouse to mouse.

In another experiment, they infected a dish of human intestinal cells with BANAL-236 and then used the new viruses produced by the cells to infect new dishes.

But for both experiments, Dr. Eloit and his colleagues opposed going up to 11 transfers, stopping at six.

“From a purely scientific point of view, we wanted to do more than six passages,” said Dr. Eloit. “But we didn’t want to take the risk of adapting a bat virus to humans.”

BANAL-236 did not retain a furin cleavage site in any of the experiments. The virus acquired other mutations, but they didn’t make it any better at infecting mouse lungs.

Scientists have been conducting such evolutionary experiments — known as “serial passage” — for more than a century. In fact, vaccines for a number of viruses, such as yellow fever, were produced by laboratory breeding: the viruses evolved in petri dishes into milder forms that were safe to inject into humans.

However, in 2011, controversy erupted over the safety of serial passage experiments that could yield new human pathogens. At the time, researchers were studying how influenza viruses, which cause intestinal infections in birds, can evolve into airborne forms that can infect humans.

Two teams of researchers sprayed bird flu viruses up the noses of ferrets, waited for the viruses to multiply, and then transmitted the new viruses to new ferrets. Soon the viruses evolved to better replicate in the ferrets.

Some critics said the research was so reckless it shouldn’t be published for fear other researchers would copy the work and inadvertently unleash a new strain of pandemic flu. The United States government halted experiments like this in order to develop a new policy for assessing their safety.

Some of the studies have restarted in recent years. But dr Stanford’s Relman and others have complained that the current regulations are not transparent enough.

dr Eloit said a committee at the Pasteur Institute that reviews potentially risky biological research approved his team’s proposal to study the new bat viruses. The scientists then ran their experiments at the same level of safety as their other work with the coronaviruses, known as Biosafety Level 3 or BSL-3.

dr Tom Inglesby, director of the Johns Hopkins Center for Health Security at the Bloomberg School of Public Health, said it’s good that scientists have given some thought to these potential risks. But he also said he wanted to see a clear justification for the decision that six passages were safe.

“It’s not possible to know in advance whether these experiments would result in more transmissible or more virulent viruses,” he said. “There’s no hard and fast rule that six is ​​safe and no more.”

But Thomas Peacock, a virologist at Imperial College London, said he thinks Dr. Eloit and his colleagues had been sufficiently careful. He pointed out that in previous studies, researchers had found that antibodies produced by humans during Covid infection were very strong against BANAL-236. That most likely meant that if the virus did leak out of a lab, it couldn’t spread very far.

“This virus would likely hit a brick wall in the general population,” said Dr. Peacock. “I don’t really have a big problem with the experiments.”

Other researchers agreed with Dr. Eloit admits that the research could shed light on how and when SARS-CoV-2 spread to humans.

for dr Eloit suggests his team’s inability to engineer a furin cleavage site on BANAL-236 in mice or human gut cells suggests that the SARS-CoV-2 lineage acquired the furin site in bats before spilling over to humans. He said it wouldn’t have been easy for the virus to find a furin site after jumping into another animal species – sometimes called “intermediate hosts” – like those being sold at a market in Wuhan, China. “I don’t see any strong case for an intermediate host,” said Dr. Eloit.

But scientists who favor the market scenario see the new results in a different light. If the researchers could not stimulate BANAL-236 to evolve the furin site during serial passage experiments, then it is unlikely that scientists in a Wuhan lab could have done so with SARS-CoV-2, as some “lab leak” proponents have done. proposed theory.

“This is another nail in the coffin of the lab leak theory, which should be firmly sealed in the crypt by now,” said Edward Holmes, a virologist at the University of Sydney.

dr Peacock was reluctant to draw firm conclusions from such small experiments. “I think it’s quite difficult to ask to get a furin site after a few passages,” he said.

dr Eloit and his colleagues are now investigating the possibility that SARS-CoV-2 ancestors preserved a furin cleavage site in wild bats. The virus could then have spread to an intermediate host or directly to people who are exposed to bats — like those who collect bat guano, hunt bats, or eat them.

To test this idea, scientists are working to obtain more samples from bats in Laos and neighboring countries. dr Eloit can’t say if their hypothesis is more likely than the others, but at least it’s one they can investigate.

“Our work as scientists,” he said, “is to explore the working hypotheses that we can explore.”

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