Thread by @Ayjchan

It looks like the universe will not let me have a day off.

@Nature just released an Addendum on the WIV's first paper about COVID, explaining what's up with RaTG13, the bat coronavirus most closely related to SARS-CoV-2. nature.com/articles/s4158…

tldr from the Mojiang mine, 293 CoVs found, 9 were SARS CoVs, 1 was RaTG13 first published in 2016 (not cited in their original 2020 @Nature paper). The other 8 SARS CoVs? We have no insight to their sequences!

Why are we hearing about this in mid-Nov 2020 when their paper was released in January, saying that they first found a match in the RdRp between RaTG13 and SARS-CoV-2 and then full genome sequenced RaTG13 to find a 96.2% genome identity match?

Furthermore, the Addendum doesn't explain why the published sequence doesn't match the raw metagenomic and amplicon sequencing trace data. How sure are we that this virus was not synthesized/cultured in the lab, a few base changes were observed and updated in the final genome?

ALSO 13 serum samples were collected from the 4 miners. And apparently these samples still exist and could be re-tested in 2020. Sure, these patients were not infected by SARS-CoV-2 but what about other SARS viruses?

How did they get from "We suspected that the patients had been infected by an unknown virus" to "the fungus turned out to be the pathogen that had sickened the miners, she says it would have been only a matter of time before they caught the coronaviruses" scientificamerican.com/article/how-ch…

I feel like we're playing a game of half-truths. "serum samples collected from 4 patients.. none of the samples gave a positive result (nucleocapsid, SARSr-CoV Rp3)"

Medical thesis: "WIV tested patients serum IgM, positive for virus"

PhD thesis: "4 people had SARS IgG"

郭 (Guo), male, 45 years, consulted Zhong Nanshan on June 19, 2012, died August 13, 2012
刘 (Liu), male, 46 years, consulted Zhong Nanshan on June 19, 2012, discharged Sep 10, 2012
吴 (Wu), male, 30 years, discharged May 28, 2012
李 (Li), male, 32 years, discharged May 28, 2012

PhD thesis from the Chinese CDC Director's lab: 4 people carried SARS IgG antibodies; the 2 discharged patients had higher antibody levels, and the 2 hospitalized patients had lower antibody levels

The lab that performed these tests? The WIV.

Another 4 miners who did not get sick were also tested by Dr. Zhong Nanshan's lab. We do not know whether these miners also had SARS targeting antibodies.

Another interesting line from this PhD thesis from the Chinese CDC Director's lab:

"... the coronavirus spike needs to be cleaved into S1 & S2... the virus is only infectious after this."

Does anyone believe me yet that we need to see what exactly were the communications between the authors, journals, and peer reviewers since January?

I cannot believe that scientific journals are the gatekeepers of info pertinent to national security.

https://twitter.com/Ayjchan/status/1320344055230963712

This Addendum is the result of months of back and forth between the authors, @nature and peer reviewers. Does the public have no right to see these exchanges? If there is more information regarding discrepancies in the initially published RaTG13 sample history and sequence?

(1) RaTG13 sequenced years earlier than described & disintegrated.
(2) It is connected to SARS-like cases in Mojiang mine, 2012. Connection was obscured.
(3) There are 8 more SARS CoVs from that cave - no published sequences.
(4) First RaTG13 genome didn't match the raw data.

Aside from these disturbing discrepancies in the sample history and data x published genome of RaTG13, please also see these interesting changes in the conclusion of the Zhou et al. @nature paper over its 9 days from submission to acceptance...

https://twitter.com/Ayjchan/status/1320347908252831744

The Jan 23 preprint ended with:
"almost identical sequences of this virus in different patients imply a probably recent introduction in humans..."

@Nature paper instead concludes: "strict regulations against the domestication and consumption of wildlife should be implemented."

In the concluding paragraph, preprint says "we still don’t know if this virus continue evolving and become more transmissible between human-to-human"

@nature paper replaces that line with "the virus is becoming more transmissible between humans" - where's the evidence for this?

Both versions: "The major differences in the sequence of the S gene of 2019-nCoV are the three short insertions in the N-terminal domain as well as changes in four out of five of the key residues in the receptor-binding motif"

What about the FCS?

I'm just saying, if SARS2 had a 100% natural origin, why would one of the top SARS labs in the world gloss over the obviously novel S1/S2 FCS insertion in the new virus, and obfuscate the sample history of the 96% identical RaTG13/4991 (connection to SARS-like cases in 2012)?

Discovered a novel SARS virus with never-seen-before FCS insertion in SARSCoVs. No need to mention that.

96% match to 1 of 9 SARS viruses from a mine that labs been persistently sampling since 2013 due to unresolved SARS-like cases. Write paper like RaTG13 sequenced post-covid.