It’s a widely accepted hypothesis that it was lab created.
No it’s not. It’s been repeatedly debunked. Check your facts
www.factcheck.org/2021/06/scicheck-the-facts-and-gaps-on-the-origin-of-the-coronavirus/
“Viral Genome Almost Certainly Not Engineered
Early in the pandemic we repeatedly debunked baseless conspiracy theories circulating on social media about SARS-CoV-2 being bioengineered.
For example, there were bogus claims that the virus contains HIV “insertions” and false claims that the virus was created by a prominent Harvard chemist who was charged by the Department of Justice on Jan. 28, 2020, for making false statements about his ties to China.
Many scientists remain open to a lab escape of a natural virus, but fewer entertain the notion that SARS-CoV-2 was engineered. While this cannot be ruled out entirely, multiple coronavirus experts view this as implausible.
“I am completely confident that the virus was not engineered,” University of Pennsylvania coronavirus researcher Susan Weiss told us in an email.
University of Utah’s Goldstein said it was “virtually impossible,” while Dr. Stanley Perlman, a coronavirus researcher at the University of Iowa, went with “impossible.”
In March, a group of scientists, including Kristian Andersen of Scripps Research and Garry of Tulane, published a paper in Nature Medicine that combed through the genome sequence for any signs of lab tinkering and concluded there were none.
Initially, the researchers had been suspicious that there were elements that were engineered. But upon closer examination, the group rejected that hypothesis, as we have written. (Contrary to some suggestions, the Andersen paper was not just an opinion piece that had no vetting by other scientists. A spokesperson for Nature Medicine told FactCheck.org by email that the paper was peer-reviewed.)
Even if scientists used methods that would not leave a trace of manipulation, as some lab leak proponents have suggested, that would still leave the arguably insurmountable problem of not knowing enough to create the virus.
“No one would know how to do it,” Perlman said. “If one doesn’t have the virus in hand, how do you decide to make this?”
Recently, there has been additional speculation about SARS-CoV-2’s furin cleavage site, which is a spot on the virus’s spike protein that’s cut by the enzyme furin to activate the spike and prepare the virus for entering cells. Experiments have shown the site is required for the virus to infect human lung cells and for viral transmission in ferrets. At first glance, the site is potentially curious, as it’s absent in coronaviruses that are closely related to SARS-CoV-2.
Furin cleavage sites, however, exist in many other coronaviruses, such as feline coronaviruses and the virus that causes MERS. Because similar sequences for the cleavage site are found in other coronaviruses, “its presence is not at all suspicious or indicative of lab manipulation,” Robertson said.
“The lineage SARS-CoV-2 emerged from is under-sampled so it’s not surprising there’s some unique properties in its genome,” he added.
Thomas Gallagher, a professor of microbiology and immunology at Loyola University Chicago who studies coronaviruses, also said he did not think the furin cleavage site was a sign of engineering.
“Some coronaviruses naturally have furin cleavage sites, others do not,” he told us in an email. “These cleavage sites evolve naturally under various natural selective pressures. The selective pressures are often powerful, so the furin cleavage site is a hotspot for coronavirus variation.”
In a self-published story on Medium, later posted on the Bulletin of the Atomic Scientists’ website, former New York Times journalist Nicholas Wade zeroed in on an ostensibly suspicious element of the furin cleavage site. Namely, that the underlying genetic sequence of the virus’s cleavage site looked manipulated because of two CGG stretches that code for the amino acid arginine. Because CGG is not often found in coronaviruses, he argued, instead of evolving naturally, it was more likely that a scientist had gone in and inserted the site into the genome while doing gain-of-function research.
In support of his theory, Wade quoted David Baltimore, Nobel laureate and president emeritus of CalTech, as saying the furin cleavage site with its arginine codons was the “smoking gun for the origin of the virus” and that it made “a powerful challenge to the idea of a natural origin for SARS2.”
But on Twitter, Andersen pushed back, noting that while rare, CGG triplets are not unheard of in SARS-CoV-2’s genetic sequence and are used to code for arginine 3% of the time. Indeed, some feline coronaviruses differ there from SARS-CoV-2 by just one nucleotide. And now that the world is awash in SARS-CoV-2 sequences, there’s no sign of the virus mutating away from using those triplets at the cleavage site, which might be expected if the sequence was unnatural.
Informed of Andersen’s points, Baltimore told a journalist with Nature that he agreed that the site could have evolved naturally. FactCheck.org contacted Baltimore as well and in an email he acknowledged he “shouldn’t have used the phrase ‘smoking gun’ because it sounds so definitive,” although he added that he didn’t think Andersen “is giving enough credence to the possibility that the furin cleavage site had a non-natural origin.”
Virologists, however, say there are plenty of other reasons why it’s incredibly unlikely that the furin cleavage site was engineered, starting with the fact that the site is not a very good cleavage site.
“This is a pretty bad one; it’s not cleaved very efficiently by furin,” Goldstein said.
In fact, he said that based on other coronaviruses with similar cleavage sites, it’s known that mutations that make the protein sequence closer to the SARS-CoV-2 sequence end up losing the ability to be cut.
“If you’re trying to insert a furin cleavage site,” Goldstein said, “why would you pick a furin cleavage site that is not actually a functional furin cleavage site in other viruses?”
Additionally, the cleavage site exists as an insertion in the genome that strangely breaks up the triplets in what is called an “out-of-frame” insertion. Any scientist wanting to add a furin cleavage site “would just plop it in nice and clean,” Goldstein said. “I don’t how to explain from a scientific standpoint how ridiculous this is, the idea that you would do an out-of-frame insertion. It just makes no sense.”
Garry, the Tulane virologist, was also baffled by the suggestion that the cleavage site sequence showed the virus had been engineered. “Which graduate student or post doc would think to put it in out-of-frame? That part I just don’t get,” he said. “This, for all the world, looks like a natural virus.”
Another line of speculation is that instead of a scientist deliberately choosing what to modify, the virus was serially passaged through human cells or an animal. That, in theory, would eliminate the requirement for a scientist to know what to insert or change. Lab leak proponents often cite experiments with human cells or humanized mice as a potential way this could happen.
But Perlman, who has done experiments passaging coronaviruses in mice, said that would not work. “Most of the time when you take viruses and pass them in tissue culture cells, you get cells that grow very well in tissue culture cells and nowhere else,” he said. And humanized mice are still mostly mice, he said, so the virus would adapt to growing better in mice, not humans.
“It’d have to be something nearer to a palm civet cat, which is a weird animal to be passaging it [the virus],” Perlman explained.
You’d also need a starting virus that is much closer to SARS-CoV-2 than any known virus, he said, and even then, the virus you’d end up with would almost certainly not be SARS-CoV-2.
As a result, Perlman said, such a scenario could be technically possible but is extraordinarily improbable. In his mind, the engineering scenario can be ruled out, although he still considered accidental release of a natural virus as an unlikely, but possible, pathway.
Further complicating the lab leak scenarios is that when SARS-CoV-2 is grown in the standard cells used to isolate and propagate viruses in the lab, the furin cleavage site is frequently lost, as is documented in multiple reports. The Shi lab, notably, used those cells with each of the three SARS-related bat coronaviruses it successfully isolated in the past.
Some have also argued that SARS-CoV-2 was too well adapted to infecting humans at the start of the pandemic — and that this could indicate human design.
But Penn State’s Boni said that’s a faulty line of thinking.
“There’s no guarantee that something that crosses over has to be perfectly adapted or half adapted or a third adapted. Whatever happens, happens,” he said.
The H1N1 swine flu pandemic in 2009, for example, he said, was very well adapted to humans and took off very easily and very quickly. “It is not a sign that they were bioengineered,” Boni said.
A paper he co-authored with Robertson in PLOS Biology pieced together SARS-CoV-2’s evolutionary history and suggests that the virus’s ability to infect a broad range of mammals evolved hundreds of years ago.
“This would indicate that the SARS-CoV-2 progenitor did not have to adapt to humans much, if at all,” Robertson said, because it had already become a “generalist virus” long ago, although he said an intermediate animal could very well still be involved in the transfer to a human.”