Animal Passage

Ten years ago, the viral pathogen most in the news was not a coronavirus but influenza—in particular, a strain of flu, designated H5N1, that arose in birds and killed a high proportion of those who were infected. For a while, the virus made headlines. Then it became clear that nearly everyone who caught the bird-flu virus got it directly from handling birds. To cause a plague, it’s not enough that a virus is an efficient killer. It also has to pass easily from one person to the next, a quality called transmissibility.

Around this time, Ron Fouchier, a scientist at Erasmus University in Holland, wondered what it would take for the bird flu virus to mutate into a plague virus. The question was important to the mission of virologists in anticipating human pandemics. If H5N1 were merely one or two steps away from acquiring human transmissibility, the world was in danger: a transmissible form of H5N1 could quickly balloon into a devastating pandemic on the order of the 1918 flu, which killed tens of millions of people.

To answer the question, scientists would have to breed the virus in the lab in cell cultures and see how it mutated. But this kind of work was difficult to carry out and hard to draw conclusions from. How would you know if the end result was transmissible?

The answer that Fouchier came up with was a technique known as “animal passage,” in which he mutated the bird-flu virus by passing it through animals rather than cell cultures. He chose ferrets because they were widely known as a good stand-in for humans—if a virus can jump between ferrets, it is likely also to be able to jump between humans. He would infect one ferret with a bird-flu virus, wait until it got sick, and then remove a sample of the virus that had replicated in the ferret’s body with a swab. As the virus multiplies in the body, it mutates slightly, so the virus that came out of the ferret was slightly different from the one that went into it. Fouchier then proceeded to play a version of telephone: he would take the virus from the first ferret and infect a second, then take the mutated virus from the second ferret and infect a third, and so on.

After passing the virus through 10 ferrets, Fouchier noticed that a ferret in an adjacent cage became ill, even though the two hadn’t come into contact with one another. That showed that the virus was transmissible in ferrets—and, by implication, in humans. Fouchier had succeeded in creating a potential pandemic virus in his lab.

When Fouchier submitted his animal-passage work to the journal Science in 2011, biosecurity officials in the Obama White House, worried that the dangerous pathogen could accidentally leak from Fouchier’s lab, pushed for a moratorium on the research. Fouchier had done his work in BSL-2 labs, which are intended for pathogens such as staph, of moderate severity, rather than BSL-4, which are intended for Ebola and similar viruses. BSL-4 labs have elaborate safeguards—they’re usually separate buildings with their own air circulation systems, airlocks and so forth. In response, the National Institutes of Health issued a moratorium on the research.

What followed was a fierce debate among scientists over the risks versus benefits of the gain-of-function research. Fouchier’s work, wrote Harvard epidemiologist Marc Lipsitch in the journal Nature in 2015, “entails a unique risk that a laboratory accident could spark a pandemic, killing millions.”

Lipsitch and 17 other scientists had formed the Cambridge Working Group in opposition. It issued a statement pointing out that lab accidents involving smallpox, anthrax and bird flu in the U.S. “have been accelerating and have been occurring on average over twice a week.”

“Laboratory creation of highly transmissible, novel strains of dangerous viruses… poses substantially increased risks,” the statement said. “An accidental infection in such a setting could trigger outbreaks that would be difficult or impossible to control. Historically, new strains of influenza, once they establish transmission in the human population, have infected a quarter or more of the world’s population within two years.” More than 200 scientists eventually endorsed the position.

The proponents of gain-of-function research were just as passionate. “We need GOF experiments,” wrote Fouchier in Nature, “to demonstrate causal relationships between genes or mutations and particular biological traits of pathogens. GOF approaches are absolutely essential in infectious disease research.”

The NIH eventually came down on the side of Fouchier and the other proponents. It considered gain-of-function research worth the risk it entailed because it enables scientists to prepare anti-viral medications that could be useful if and when a pandemic occurred.

By the time NIH lifted the moratorium, in 2017, it had granted dozens of exceptions. The PREDICT program, started in 2009, spent $200 million over 10 years, sending virologists all over the world to look for novel viruses and perform gain-of-function research on them. The program’s funding ran out in 2018 and it wasn’t renewed. Early this year, after the Trump administration drew criticism for canceling the program, it granted a six-month extension.

By the time the current pandemic hit, animal-passage experiments had become commonplace. Scientists in many of the more than 30 BSL-4 labs around the world had used them to enhance the transmissibility of respiratory-tract pathogens.

Did the work help during the current pandemic? In a recent article in the Lancet, Colin Carlson, an expert in emerging infectious diseases at Georgetown University, argued that work funded by PREDICT helped virologists rapidly isolate and classify the SARS-CoV-2 virus when it came out. However, the research “could have been better positioned for an overall impact.” Although the program found hundreds of new viruses, it’s nearly impossible for scientists to assess their risk to humans. The only way to tell is to “observe a human infection.”

Richard Ebright, an infectious disease expert at Rutgers, put it more bluntly. “The PREDICT program has produced no results—absolutely no results—that are of use for preventing or combating outbreaks. There’s no information from that project that will contribute in any way, shape or form to addressing the outbreak at hand. The research does not provide information that’s useful for developing antiviral drugs. It does not provide information that’s useful for developing vaccines.”

China’s role

The Wuhan Institute of Virology is one of many labs to receive PREDICT funding. Shi Zheng-Li, a virologist known as “bat woman” for her group’s work in collecting hundreds of coronaviruses, and her staff at the Institute explored the same bat caves that were thought to have given rise to the original SARS virus in 2002. Her scientists penetrated remote caves, swabbing bats’ anuses and collecting their excretions. When they returned to the lab, they cultured the viruses they found, determined their genomic sequences and tried to determine how they infect cells and animals in the lab.

The Institute began a program of gain-of-function research into bat coronaviruses in 2015. That involved taking selected strains and seeking to increase the ability of those viruses to transmit from one person to another. The gain-of-function research went hand-in-hand with the surveillance project. As scientists identified new classes of bat viruses that have the ability to infect human cells, that raised the question of what changes would have to arise in nature to make that virus transmissible in humans, which would pose a pandemic threat.

In 2015, the Wuhan lab performed a gain of function experiment using cut-and-paste genetic engineering, in which scientists take a natural virus and directly make substitutions in its RNA coding to make it more transmissible. They took a piece of the original SARS virus and inserted a snippet from a SARS-like bat coronavirus, resulting in a virus that is capable of infecting human cells. A natural virus altered with these methods would be easily flagged in a genetic analysis, like a contemporary addition to an old Victorian house.

A virus produced with animal passage methods would be much harder to spot. These viruses are not directly manipulated. When the virus passes from one animal to the next, it undergoes something similar to what would happen in the wild during the course of its evolution. A wild coronavirus passed through 10 ferrets would be difficult to identify as having been engineered or manipulated.

There is no published record of animal-passage work on coronaviruses in the Wuhan Institute. The lab got its first BSL-4 lab in 2018, which is now considered a requirement for this kind of work (though some work proceeds in BSL-3-enhanced labs). It’s possible that researchers started animal passage work in the BSL-4 lab but didn’t finish it in time to publish before the current pandemic, when China tightened up on publications. It’s possible that the work was done in secret. It’s possible that it never happened at all. But some scientists think it’s unlikely that an expensive BSL-4 lab would not be doing animal-passage research, which by 2018 was not unusual.

Tracing the origins

To figure out where SARS-CoV-2 came from, Kristian Andersen of Scripps Research and his colleagues performed a genetic analysis: they published the work, which has been widely cited, on March 17 in Nature Medicine. The researchers focused on certain genetic features of the virus for telltale signs of “manipulation.”

One feature was the spike of protein that the virus uses to attach so effectively to the human body’s ACE2 receptors, a molecular feature of the cells in our lungs and other organs. The spike in SARS-Cov-2, the authors conclude, differs from that of the original SARS virus in ways that suggest it was “most likely the product of natural selection”—in other words, natural, not manipulated in a lab.

However, the paper’s reasoning as to why animal passage, in particular, can be ruled out, is not clear. “In theory, it is possible that SARS-CoV-2 acquired the… mutations during adaptation to passage in cell culture,” the authors write. The theory that the virus mutated in mammalian hosts such as pangolins “provides a much stronger… explanation.” Whether or not that includes animal passage in a lab, they don’t say. Andersen didn’t respond to Newsweek requests for comment.

Rutger’s Ebright, a longtime opponent of gain of function research, says that the Andersen analysis fails to rule out animal-passage as an origin of SARS-CoV-2. “The reasoning is unsound,” he wrote in an email to Newsweek. “Embarrassingly unsound. They favor the possibility ‘that the virus mutated in an animal host such as a pangolins’ yet, simultaneously, they disfavor the possibility that the virus mutated in ‘animal passage.’ Because the two possibilities are identical, apart from location, one can’t logically favor one and disfavor the other.”

Jonathan Eisen, an evolutionary biologist at UC Davis, says that the preponderance of evidence, while not definitive, suggests that the virus came from nature, not a lab. “There’s no hint there that there’s something unnatural, that is, genetically engineered,” he says. But “there is some wiggle room” in the findings that admits the possibility that the virus was concocted in a lab via animal passage. “Passaging is hard to test for. Escape from a lab is hard to test for,” he says. “If [Wuhan researchers] collected something from the field and they were doing some experiments in the lab with it, and some person got infected and then it spread from there, that would be really hard to distinguish from it having spread in the field directly.”

Wuhan is in possession of a virus, RATG13, that is thought to be the most similar to SARS-CoV-2 of any known virus—the two share 96 percent of their genetic material. That four-percent gap would still be a formidable gap for animal-passage research, says Ralph Baric, a virologist at the University of North Carolina who collaborated with Shi Zheng-Li on the 2015 gain-of-function research. “You keep running into problems that just don’t make it likely,” he says. Wuhan would probably have had to start with a virus closer to SARS-CoV-2 than RATG13, which is within the realm of possibilities.

“The only way to resolve it,” says Baric, “is transparency and open science and have some real investigation into it. I don’t think the Chinese are going to allow that. I don’t know what any country would do in this situation. I would like to think that the U.S. would be transparent.”

Jenni Fink contributed to this report

The post The Controversial Wuhan Lab Experiments That May Have Started the Coronavirus Pandemic appeared first on Newsweek.