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Fact Checkers rely on one source for origins of COVID19

Summary:
The recent paper by  Li-Meng Yan et al  that argues that COVID19 originated in a laboratory has been universally condemned by "fact checkers".  Li Meng Yan risked her life to bring this truth to our news media.  Facebook and other social media sites are removing coverage as "fake news".Where do the "fact checkers" get their "facts"?  It turns out that they are all using a single scientific paper  "The proximal origin of SARS-CoV-2, by Kristian Anderson et al" published in Nature and reports that reference this paper.This Nature paper is strange because in its summary it says "Our analyses clearly show that SARS-CoV-2 is not a laboratory construct or a purposefully manipulated virus." but in the paper itself it says something very different.The argument that the virus could not be made in a

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The recent paper by  Li-Meng Yan et al  that argues that COVID19 originated in a laboratory has been universally condemned by "fact checkers".  Li Meng Yan risked her life to bring this truth to our news media.  Facebook and other social media sites are removing coverage as "fake news".

Where do the "fact checkers" get their "facts"?  It turns out that they are all using a single scientific paper  "The proximal origin of SARS-CoV-2, by Kristian Anderson et al" published in Nature and reports that reference this paper.

This Nature paper is strange because in its summary it says "Our analyses clearly show that SARS-CoV-2 is not a laboratory construct or a purposefully manipulated virus." but in the paper itself it says something very different.

The argument that the virus could not be made in a laboratory is that it is not the ideal solution for infection and that a sufficiently similar base virus, the main part of the virus used as a template, has not yet been found.(Note B).

This is a very thin argument on which to condemn any competing ideas of origin.  The rebuttal is straightforward.  Anyone creating the virus would stop at "good enough" rather than ideal, especially given that a special (furin) site provides a boost to infectivity.  This simple rebuttal dispenses with the first argument.  Two contenders for the base virus have indeed been found which dispenses with the second argument (Note C and below).  

 Li-Meng Yan et al  cover these arguments in their paper and show why they are false but the fact checking sites simply ignore the possibility that the Nature paper might be wrong.

The elephant in the room when it comes to considering how the virus that causes COVID19 developed is that a senior virologist at the Wuhan Institute of Virology, Shi Zhengli, and no doubt her team, are expert at genetically manipulating the part of the virus that mediates infection, the so-called "spike".  Anderson's Nature paper failed to even mention that this was the case. Shi was part of the team in the USA that created a furore by publishing "A SARS-like cluster of circulating bat coronaviruses shows potential for human emergence" in which they genetically modified a coronavirus to considerably increase infection of humans.

The Failure of Fact Checking

You can click on the links below to check out the sources used by the "fact checking" sites, they nearly all use "The proximal origin of SARS-CoV-2" as the definitive and sole original source of the idea that the virus that causes COVID19 is not lab-made.

The Poynter Institute (politifact)   @PolitiFact

Fullfact  @FullFact

Factcheck.org  @factcheckdotorg This organisation uses the lead author of the Nature article, Kristian Anderson, to dismiss speculations about HIV sequences in the COVID virus but fails to mention that the nobel prize-winning discoverer of HIV, Professor Luc Montagnier, said that COVID19 was a lab escape. : "With my colleague, bio-mathematician Jean-Claude Perez, we carefully analyzed the description of the genome of this RNA virus,”.."in order to insert an HIV sequence into this genome, molecular tools are needed, and that can only be done in a laboratory." The HIV sequences in the COVID19 virus are real, see below.

Google fact check  - uses politifact (see above). @Google #HeyGoogle

The Snopes fact checking website again relies on Anderson's article: "These two adaptations are the features of the coronavirus that cause speculation about it being engineered to kill. The problem, according to a team of researchers who analyzed the genome of SARS-CoV-2 for a March 2020 paper in Nature Medicine, is that if someone wanted to design a virus using methods currently available to science, scientists would not have solved the problem the way nature apparently did, because scientists wouldn’t have predicted it to be a viable solution in the first place." Notice that the original paper didn't say that scientists would not have predicted the solution, just that the solution used in the virus was not ideal (Note E). #snopes

These fact checking websites are used by Facebook, Twitter etc to ban articles as fake news.  It is worrying that they themselves may be spreading fake news.

The Nature article was produced by the Scripps Institute which had been flagged in 2016 as a likely source of Chinese intervention in academic work:

Fact Checkers rely on one source for origins of COVID19

Fact checkers should also be aware that Springer Nature had already been caught out in 2017 for allowing the Chinese government to censor content for political reasons. 

The fact checkers must actually read scientific papers and check independent papers. The contribution by Li-Meng Yan et al  that suggests COVID was created in the lab is worth reading, it supports the claims that it makes.

The "withdrawn" papers on the origin of COVID19 

These have largely been withdrawn at the behest of Chinese academics.  These three crucial papers were withdrawn:

The possible origins of 2019-nCoV coronavirus. Which is a fairly innocent, early survey of the site of the outbreak in Wuhan but contains a survey of the HuaNan fish market which shows that bats were never sold there and clearly implicates poor biosafety at the virological labs in Wuhan. That the fish market was not involved was confirmed by Decoding evolution and transmissions of novel pneumonia coronavirus using the whole genomic data.

Wu et al (republished after correction) which shows that base viruses - backbones - are available (although the Nature paper itself also mentioned a likely backbone).

Uncanny similarity of unique inserts in the 2019-nCoV spike protein to HIV-1 gp120 and Gag which shows that HIV sequences are in the virus. A later paper by different authors confirmed this - see  HIV-1 did not contribute to the 2019-nCoV genome - they confirm the HIV sequences are present although they cannot account for them all and are a Chinese group hoping to quash theories that the virus was man-made. 

More detail on "The proximal origin of SARS-CoV-2"

The first contender for a base virus (the "backbone") was discovered by Wu et al and this was published on 3rd of February online although it was probably communicated to other workers from 7th January.  The authors of the Nature article themselves mention a possible viral backbone called RaTG13 (Note C), so undermining their own argument. They strangely reason that because the infective part of the virus - the bit that is not the backbone - is not the same as the COVID19 virus RaTG13 cannot be the backbone.  A weird argument when a lab-made COVID19 virus would consist of the backbone plus a lab-made infective part.

The Nature article largely blames pangolins for incubating the virus even though a paper published several weeks previously emphatically showed that pangolins were not vectors (Note D).

Text from the Nature Article

(A) What is special about the virus that causes COVID19

 "(i) on the basis of structural studies and biochemical experiments, SARS-CoV-2 appears to be optimized for binding to the human receptor ACE2; and

(ii) the spike protein of SARS-CoV-2 has a functional polybasic (furin) cleavage site at the S1–S2 boundary through the insertion of 12 nucleotides, which additionally led to the predicted acquisition of three O-linked glycans around the site."

(B) The argument that the virus cannot be laboratory made

"It is improbable that SARS-CoV-2 emerged through laboratory manipulation of a related SARS-CoV-like coronavirus. As noted above, the RBD of SARS-CoV-2 is optimized for binding to human ACE2 with an efficient solution different from those previously predicted. 

Furthermore, if genetic manipulation had been performed, one of the several reverse-genetic systems available for betacoronaviruses would probably have been used. However, the genetic data irrefutably show that SARS-CoV-2 is not derived from any previously used virus backbone."

(C) The authors mention a possible viral backbone

"As many early cases of COVID-19 were linked to the Huanan market in Wuhan, it is possible that an animal source was present at this location. Given the similarity of SARS-CoV-2 to bat SARS-CoV-like coronaviruses, it is likely that bats serve as reservoir hosts for its progenitor. Although RaTG13, sampled from a Rhinolophus affinis bat, is ~96% identical overall to SARS-CoV-2, its spike diverges in the RBD, which suggests that it may not bind efficiently to human ACE27 (Fig. 1a)"

(D) Pangolins

"Malayan pangolins (Manis javanica) illegally imported into Guangdong province contain coronaviruses similar to SARS-CoV-2. Although the RaTG13 bat virus remains the closest to SARS-CoV-2 across the genome, some pangolin coronaviruses exhibit strong similarity to SARS-CoV-2 in the RBD, including all six key RBD residues (Fig. 1). This clearly shows that the SARS-CoV-2 spike protein optimized for binding to human-like ACE2 is the result of natural selection."

(E) That the binding "spike" protein is not ideal

"While the analyses above suggest that SARS-CoV-2 may bind human ACE2 with high affinity, computational analyses predict that the interaction is not ideal and that the RBD sequence is different from those shown in SARS-CoV to be optimal for receptor binding."

17/9/20

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