Claim: WIV removed virus sequences from public database

Mendel

Mendel

Senior Member.

A Coverup?


Article:

U.S. Confirms Removal of Wuhan Virus Sequences from Database​

Details of the genetic makeup of some of the earliest samples of coronavirus in China were removed from an American database where they were initially stored, at the request of Chinese researchers, U.S. officials confirmed, adding to concerns over secrecy surrounding the outbreak and its origins.

The data, first submitted to the U.S.-based Sequence Read Archive in March 2020, were “requested to be withdrawn” by the same researcher three months later in June, the U.S. National Institutes of Health said in a statement Wednesday. The genetic sequences came from the Chinese city of Wuhan where the Covid-19 outbreak was initially concentrated.
(via @Agent K)

Article:
About a year ago, more than 200 data entries from the genetic sequencing of early cases of Covid-19 in Wuhan disappeared from an online scientific database.

Now, by rooting through files stored on Google Cloud, a researcher in Seattle reports that he has recovered 13 of those original sequences — intriguing new information for discerning when and how the virus may have spilled over from a bat or another animal into humans.

The new analysis, released on Tuesday, bolsters earlier suggestions that a variety of coronaviruses may have been circulating in Wuhan before the initial outbreaks linked to animal and seafood markets in December 2019.
(via @Lu Ann Lewellen)

No Coverup.



Article:
The story began in early 2020, when researchers at Wuhan University investigated a new way to test for the deadly coronavirus sweeping the country. They sequenced a short stretch of genetic material from virus samples taken from 34 patients at a Wuhan hospital.

The researchers posted their findings online in March 2020. That month, they also uploaded the sequences to an online database called the Sequence Read Archive, which is maintained by the National Institutes of Health, and submitted a paper describing their results to a scientific journal called Small. The paper was published in June 2020. [...]

At the time, a spokeswoman for the N.I.H. said that the authors of the study had requested in June 2020 that the sequences be withdrawn from the database. The authors informed the agency that the sequences were being updated and would be added to a different database. (The authors did not respond to inquiries from The Times.)

On July 5, more than a year after the researchers withdrew the sequences from the Sequence Read Archive and two weeks after Dr. Bloom’s report was published online, the sequences were quietly uploaded to a database maintained by China National Center for Bioinformation by Ben Hu, a researcher at Wuhan University and a co-author of the Small paper.

On July 21, the disappearance of the sequences was brought up during a news conference in Beijing, where Chinese officials rejected claims that the pandemic started as a lab leak.

According to a translation of the news conference by a journalist at the state-controlled Xinhua News Agency, the vice minister of China’s National Health Commission, Dr. Zeng Yixin, said that the trouble arose when editors at Small deleted a paragraph in which the scientists described the sequences in the Sequence Read Archive.

“Therefore, the researchers thought it was no longer necessary to store the data in the N.C.B.I. database,” Dr. Zeng said, referring to the Sequence Read Archive, which is run by the N.I.H.

An editor at Small, which specializes in science at the micro and nano scale and is based in Germany, confirmed his account. “The data availability statement was mistakenly deleted,” the editor, Plamena Dogandzhiyski, wrote in an email. “We will issue a correction very shortly, which will clarify the error and include a link to the depository where the data is now hosted.”

The journal posted a formal correction to that effect on Thursday.

On their own, these sequences can’t resolve the open questions about how the pandemic originated, whether through a contact with a wild animal, a leak from a lab or some other route.


Excerpted:
Article:
But the sequence of that bat virus found in 2013 differs from SARS-CoV-2 by about 1100 nucleotides, which means decades must have passed before it evolved into the pandemic coronavirus—and other species may well have been infected with the bat virus before it made the final jump into people. This great difference in sequences, says evolutionary biologist Andrew Rambaut at the University of Edinburgh, means researchers cannot use a few mutations like the ones Bloom highlights to look back in time to see the "roots" of the family tree of SARS-CoV-2 tree.

Rambaut notes that the Chinese researchers submitted their Small paper before requesting that the SRA remove the data. "The idea that the group was trying to hide something is farcical," Rambaut says. "If they were covering something [up] they surely would have not submitted the paper. … I don't like the insinuations about malfeasance where [Bloom] has zero knowledge of the reasons the authors of the paper had for removing their data."

Others are underwhelmed. "Jesse is resurfacing info that's been online for over a year and claiming it proves a cover-up," says Stephen Goldstein, an evolutionary virologist at the University of Utah. "I don't understand [his reasoning]." The Small paper is simply a good study that "unfortunately flew below the radar," he adds.

Bloom acknowledges that researchers can piece together the coronavirus sequences from the data found in the Small paper.


Conclusion


• it wasn't really a cover-up,
• the data is back online,
• there were no bombshell revelations = there was no reason to cover anything up.
 
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Shi's work raised suspicions when she admitted that some of the work was done in BSL-2 labs, and when it was revealed that she had worked with a deadly coronavirus 96% similar to SARS-CoV-2 since 2016 under a different name.

Article:

How I Learned to Stop Worrying And Love the Lab-Leak Theory*​

Dr. Shi herself later told Scientific American that, when news of the new virus erupted, her first fear was that it had come from her institute. She did not sleep for days, she said, until she had finished checking her lab’s logs and assured herself that it had not.

Since then, though, more has come to light about the work done by Dr. Shi’s teams.

The most startling bit of information was that, rather than “finding” RaTG13 in her freezers in February, Dr. Shi had worked with it since at least 2016, but under a different name, RaBtCoV/4991.

RaBtCoV/4991 had not been gathered at random but from a mineshaft in which miners digging bat guano got pneumonia, some fatally. Dr. Shi’s lab sequenced enough of it to be able to say it was the most “SARS-like” of the viruses from that investigation.

There were arguments over whether the miners died of fungal pneumonia, viral pneumonia or both, but that link made it a likely suspect for any lab wanting to explore dangerous viruses. Not mentioning her previous work with it was troubling.

Also, Dr. Shi was trained by Ralph S. Baric of the University of North Carolina in building “chimera” viruses — taking, for example, the spike protein from a new virus and splicing it to the backbone of a known one like SARS. He invented “no-see-um” techniques that left no trace of the splice.

(Interestingly, Dr. Baric is one of the signers of the letter to Science demanding a more thorough investigation of all Wuhan labs.)

Then, to see if the new chimeras could infect people, they were tested against human airway cells and “humanized” mice — mice bred to have human ACE-2 receptors on their organs.

Also, Dr. Shi’s teams had done work on inserting cleavage sites into viruses and seeing if that enhanced their ability to infect human cells.

All this raises a disturbing possibility: What if some Wuhan scientist did something like take the likely suspect virus RaBtCoV/4991 and use it as the “backbone” for a set of chimeras with different receptor binding domains?
...
Jon Cohen of Science magazine put essentially these very questions to Dr. Shi back in August, 2020.

She said no such work took place in her lab, and that the RaBtCoV/4991 virus had only been sequenced, not isolated or grown out as a virus before the sample was used up. Everyone in her lab had tested negative for antibodies to SARS-like coronaviruses so there was no evidence of an outbreak inside, she said. And she had been assured through regular conversations with other Wuhan labs that that they had no leaks either.

Doubts have been raised about that, including the question: since Covid-19 was racing through Wuhan in early 2020, how likely would it be that no one in her lab tested antibody-positive? Wouldn’t some have gotten infected outside?

Ultimately, much of the debate comes down to this: Is Dr. Shi telling the whole truth? And even if she is, are all her similarly skilled colleagues in Wuhan? Are they being allowed to do so by their government — which has a history of silencing scientists?
...
I spoke about Nick Wade's article last week with Dr. W. Ian Lipkin, the renowned Columbia University virus hunter who was one of the five co-authors on the seminal “proximal origin” paper.

He favored a natural origin theory, he said, in part because he had assumed that all the Wuhan Institute’s 2019 work with SARS-like viruses had been done in its top-level BSL-4 lab, which was cleared to operate in 2017. (State Department cables from 2018 raised questions about how well-run the lab was.)

But later he learned of studies with Dr. Shi’s name on them showing that work he considers dangerous had been done in level BSL-2 labs, which he considers highly porous to leaks, not just in 2016, but in 2020.

“That’s screwed up,” he said. “It shouldn’t have happened. People should not be looking at bat viruses in BSL-2 labs. My view has changed.”
 
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Uh, yeah. And some people thought we should nuke Beijing.

Based on the available facts, the answer seems clear enough: Andersen, Garry, and the others looked more closely at the data, and decided that their fears about a lab leak had been unwarranted; the viral features were simply not as weird as they’d first thought. The political conversation around this episode is not so easily summarized, however. Yesterday’s hearing was less preoccupied with the small, persistent possibility that the coronavirus really did leak out from a lab than with the notion of a conspiracy—a cover-up—that, according to Republicans, involved Fauci and others in the U.S. government swaying Andersen and Garry to leave behind their scientific judgment and endorse “pro-China talking points” instead. (Fauci has denied that he tried to disprove the lab-leak theory.)

https://www.theatlantic.com/science/archive/2023/07/covid-lab-leak-congress-investigation/674690/
Content from External Source
 
deirdre said:
what people?
Click to expand...

A few on Facebook that I saw. I don't know of anyone in government who thought that. I didn't mean to imply there were. There were verbal attacks on Beijing certainly:

BEIJING (Reuters) - China accused U.S. Secretary of State Mike Pompeo of telling one lie to cover up another in his continued attacks against Beijing over the coronavirus pandemic.

The remarks were made by Chinese foreign ministry spokeswoman Hua Chunying, who reiterated that Beijing has been transparent about the COVID-19 outbreak that emerged in China late last year and that U.S. politicians are making baseless accusations against China.

https://www.reuters.com/article/hea...ver-its-handling-of-coronavirus-idINKBN22J13P
Content from External Source
I was wondering if we were going to have a war on top of the pandemic.
 
Lu Ann Lewellen said:
I was wondering if we were going to have a war on top of the pandemic.
Click to expand...
considering most of our medical supplies (and everything else really) come from China, i dont think you have to worry about us starting a war. It's not like you can put the genie back in the bottle anyway.
 
deirdre said:
considering most of our medical supplies (and everything else really) come from China, i dont think you have to worry about us starting a war. It's not like you can put the genie back in the bottle anyway.
Click to expand...

Things got pretty hot there for a while. The blame went both ways.


BEIJING — China is pushing a new theory about the origins of the coronavirus: It is an American disease that might have been introduced by members of the United States Army who visited Wuhan in October.

There is not a shred of evidence to support that, but the notion received an official endorsement from China’s Ministry of Foreign Affairs, whose spokesman accused American officials of not coming clean about what they know about the disease.

https://www.nytimes.com/2020/03/13/world/asia/coronavirus-china-conspiracy-theory.html
Content from External Source
Did any mobs go after the bats with torches and pitchforks?
 
deirdre said:
mobs went after the CHinese with torches and pitchforks?
Click to expand...

Not the Chinese, I meant the bats that were thought to be the source of the virus. I hope they didn't. Bats are beneficial.

Research evidence suggests that SARS-CoV and MERS-CoV originated in bats. SARS-CoV then spread from infected civets to people, while MERS-CoV spreads from infected dromedary camels to people. To date, the origin of SARS-CoV-2 which caused the COVID-19 pandemic has not been identified. The scientific evidence thus far suggests that SARS-CoV-2 likely resulted from viral evolution in nature and jumped to people or through some unidentified animal host. Public health and scientific organizations are engaged in a continued international effort to uncover the origins of SARS-CoV-2, which is essential to preventing future pandemics.

https://www.niaid.nih.gov/diseases-conditions/origins-coronaviruses
Content from External Source
Close relatives were found in bats in Laos so China might not even be the country of origin.

Scientists have found three viruses in bats in Laos that are more similar to SARS-CoV-2 than any known viruses.

https://www.nature.com/articles/d41586-021-02596-2
Content from External Source
 
Agent K said:
All this raises a disturbing possibility: What if some Wuhan scientist did something like take the likely suspect virus RaBtCoV/4991 and use it as the “backbone” for a set of chimeras with different receptor binding domains?
Content from External Source
Click to expand...
That's not a realistic possibility, because that virus is still decades of mutations removed from SARS-CoV-2. The bat virus researchers in Laos did in fact find a bat virus in the wild that's closer to SARS-CoV-2 than RaTG13 is.
Agent K said:
But later he learned of studies with Dr. Shi’s name on them showing that work he considers dangerous had been done in level BSL-2 labs, which he considers highly porous to leaks, not just in 2016, but in 2020.
Click to expand...
It's not clear to me what the evidence is that the 2016 work was done in a BSL-2 lab, and how dangerous it really was.
I do notice that you're pivoting to another (off-)topic again after a short time when your previous claim did not pan out. You should be posting this in the "lab leak theory" thread, but not here.
 
Things had gotten tense and Dr. Shi finally spoke out. Over the past 15 years her lab had isolated and grown only three bat coronaviruses related to SARS. There was nothing to cover up.

“U.S. President Trump's claim that SARS-CoV-2 was leaked from our institute totally contradicts the facts,” she added. “It jeopardizes and affects our academic work and personal life. He owes us an apology.”

Shi stressed that over the past 15 years, her lab has isolated and grown in culture only three bat coronaviruses related to one that infected humans: the agent that causes severe acute respiratory syndrome (SARS), which erupted in 2003. The more than 2000 other bat coronaviruses the lab has detected, including one that is 96.2% identical to SARS-CoV-2, are simply genetic sequences that her team has extracted from fecal samples and oral and anal swabs of the animals. She also noted that all staff and students in her lab recently tested negative for SARS-CoV-2, challenging the notion that one of them triggered the pandemic.

Shi was particularly chagrined about the 24 April decision by the U.S. National Institutes of Health (NIH), made at the White House's behest, to ax a grant to the EcoHealth Alliance in New York City that included bat virus research at WIV. “We don't understand [it] and feel it is absolutely absurd,” she said.

Shi's responses—available in full at scim.ag/ShiZhengli—are “a big contribution,” says Daniel Lucey of Georgetown University, an outbreak specialist who blogs about SARS-CoV-2 origin issues. “There are a lot of new facts that I wasn't aware of. It's very exciting to hear this directly from her.” The answers were coordinated with public information staffers at the Chinese Academy of Sciences, of which WIV is part, and evolutionary biologist Kristian Andersen of Scripps Research suspects they were “carefully vetted” by the Chinese government. “But they're all logical, genuine, and stick to the science,” he says.

https://www.science.org/doi/10.1126/science.369.6503.487
Content from External Source
 
Agent K said:

The most startling bit of information was that, rather than “finding” RaTG13 in her freezers in February, Dr. Shi had worked with it since at least 2016, but under a different name, RaBtCoV/4991.

[..] Dr. Shi’s lab sequenced enough of it to be able to say it was the most “SARS-like” of the viruses from that investigation.
Content from External Source
Click to expand...
From the linked paper:
In the phylogenetic tree, RaBtCoV/4991 showed more divergence from human SArS-CoV than other bat SL-CoVs and could be considered as a new strain of this virus lineage
Content from External Source
So, it wasn't all that SARS-like, but because of that similarity, the sample was renamed to reflect the origin (Tongguan 2013). After the SARS-CoV-2 genome became known, this sample turned out to be the closest relative to it at WIV, but that could only be "found" in hindsight. In that sense, it was a true scientific discovery.

However, since then closer relatives of SARS-CoV-2 have been found in the wild:
Article:
Scientists from the Institut Pasteur du Laos and the Faculty of Environmental Sciences at the National University of Laos took samples from the bats. Their colleagues from the Institut Pasteur, Université de Paris and the Alfort National Veterinary School (EnvA) then sequenced the genomes of the viruses discovered. They identified three viruses in particular (BANAL-103, BANAL-236 and BANAL-52) with genomic similarities to SARS-CoV-2, especially in a key domain of the spike protein that enables the virus to bind to host cells. Using direct affinity measurements, crystallography and computational simulations of molecular dynamics, the scientists demonstrated that the affinity of these three bat coronaviruses for the human ACE2 receptor is similar to that of the SARS-CoV-2 virus, and that they are also able to enter human cells via the same receptor. The reserchers then proved that the BANAL-236 virus was effectively able to muliply within human cells.
 
Mendel said:
That's not a realistic possibility, because that virus is still decades of mutations removed from SARS-CoV-2. The bat virus researchers in Laos did in fact find a bat virus in the wild that's closer to SARS-CoV-2 than RaTG13 is.
Click to expand...
I only quoted the highlighted part for brevity, but there were more questions. I underlined the part that addresses the decades of mutations.
Article:
All this raises a disturbing possibility: What if some Wuhan scientist — someone in Dr. Shi’s lab or perhaps at the Wuhan Center for Disease Control right near the market, or possibly some military scientist she trained but could not control — did something like take the likely suspect virus RaBtCoV/4991 and use it as the “backbone” for a set of chimeras with different receptor binding domains? What if that scientist was trying in 2019 to attach binding domains from viruses recently found in dying pangolins seized from wildlife smugglers in southern China? What if someone got tempted to add a cleavage site to see if that supercharged it?
What if various such chimeras were passaged through cultures of human cells or humanized mice? Wouldn’t that speed up mutations into forms likely to infect humans even faster than nature can? Wouldn’t that mean that something that looked like the current pandemic strain could emerge, polybasic cleavage sites, O-linked glycans and all?
And what if someone doing that work in a less secure lab than should have been permitted got infected before catching the subway home?
It’s a lot of ifs, and it’s pure speculation, which has been going on since mid-last year.


Mendel said:
It's not clear to me what the evidence is that the 2016 work was done in a BSL-2 lab, and how dangerous it really was.
Click to expand...
The 2016 paper said it.
Article:
All experiments using live virus was conducted under biosafety level 2 (BSL2) conditions.

Ian Lipkin said it's dangerous. He's the expert.

Mendel said:
I do notice that you're pivoting to another (off-)topic again after a short time when your previous claim did not pan out. You should be posting this in the "lab leak theory" thread, but not here.
Click to expand...

The issue was whether to believe what Shi said, and I remembered that there was something she did that really disturbed scientists. I also remembered something being deleted from a database, so I posted about that. But then I looked back at the Timeline: How the Wuhan lab-leak theory suddenly became credible, and remembered that it was the renaming of RaBtCoV/4991 that disturbed scientists, so I posted about it here.
 
Agent K said:
It’s a lot of ifs, and it’s pure speculation
Content from External Source
Click to expand...
Yes, it is.


Agent K said:
remembered that it was the renaming of RaBtCoV/4991 that disturbed scientists
Click to expand...
but that has a perfectly good, rational reason!


Agent K said:
What if various such chimeras were passaged through cultures of human cells or humanized mice?
Click to expand...
They weren't, because the RaTG13 sample was used up after it had been sequenced; that virus was never isolated.
Passage doesn't reduce the number of generations required to introduce these more than 1000 mutations.

And moreover, the speculative passage hypothesis is unable to explain how BANAL-52, found in Laos, is 96.8% identical to SARS-CoV-2, which is closer than RaTG13's 96.1%. The passage is unlikely to mimic a mutation process taking place in the wild.

That whole, mad scientist vibe of "let's see if we can create a new pandemic" is divorced from reality.

See https://www.metabunk.org/threads/cl...t-of-wuhan-lab-not-man-made.11212/post-297046 for the full Q&A.
 
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