🧵📸 We have now solved the Pangolin Riddle!

This is BIG so sit tight!

1. WIV did have Pangolins in 2019 (we now have proof)

2. WIV isolated Pangolin/HKU4/MERS like Covs with Furin Sites in 2019, just before the pandemic!
3. Important Note

If you have not done so already, please read the linked thread above before continuing, it will make much more sense if you do so.
4. GX Pangolins at WIV in 2019!

From the Horse's Mouth in 2024!

"In 2019 & 2020, 86 anal swab samples & 80 serum samples were collected from Guangxi pangolins"

"Pangolin samples were transported & stored at Wuhan Institute of Virology, CAS"

cell.com/cell/fulltext/…Image
5. Pangolin MERS Cov Clones

Cell Paper received June 2022

WIV does not say when viral isolates from pangolin samples were obtained & experimented with

BUT research of @stevenemassey @quay_dr @Daoyu15 @humblesci @ydeigin shows that a MERS/HKU4 clone was used before Jan 2020!
@stevenemassey @quay_dr @Daoyu15 @humblesci @ydeigin 6. NCBI BioProject PRJNA602160

We identified SRA datasets with HKU4-related & MERS-related CoV sequences

Datasets generated by HZAU

Registered: 2020-01-19

Published: 2020-02-09

Discovery of a Novel MERS DNA Clone Contaminating Sequencing Datasets

fortunejournals.com/articles/disco… Image
@stevenemassey @quay_dr @Daoyu15 @humblesci @ydeigin 7. Above claims recently confirmed by WIV patent!

Also BAC finding confirmed

h/t @Rcoleptic and @Engineer2The

x.com/Engineer2The/s…

MERS cluster pangolin coronavirus MjHKU4r CoV-1replicon plasmid, cell line and application

Published in Sept 2023

patents.google.com/patent/CN11730… Image
@stevenemassey @quay_dr @Daoyu15 @humblesci @ydeigin @Rcoleptic @Engineer2The 8. Image of Replicon Plasmid from the Patent

Note Bsmb 1 restriction stes used

patentimages.storage.googleapis.com/33/e4/c9/2fc8a…Image
@stevenemassey @quay_dr @Daoyu15 @humblesci @ydeigin @Rcoleptic @Engineer2The 9. The Ubiquitous Yi-Gang Tong

Proudly discusses the mechanism by which a bat MERS-like coronavirus infects host cells

1. MjHKU4r-CoV virus discovered in GX pangolins

2. Similarities between a furin cleavage site (RQQR) in SD1 of S protein & MERS

en-life.buct.edu.cn/2024/0520/c244… Image
@stevenemassey @quay_dr @Daoyu15 @humblesci @ydeigin @Rcoleptic @Engineer2The 10. Continued

3. MjHKU4r-CoV-1 infection was significantly affected by furin protease inhibitors.

4. Mutation experiments at the furin cleavage site in the S protein of MjHKU4r-CoV-1 demonstrated the crucial role of host protease cleavage during infection. Image
@stevenemassey @quay_dr @Daoyu15 @humblesci @ydeigin @Rcoleptic @Engineer2The 11. Continued (2)

5. They used various cell lines & organoids to observe infectivity of MjHKU4r-CoV-1

6. MjHKU4r-CoV-1 can infect various human cell lines & replicate in human respiratory & intestinal organoids

7. Also in vivo infection experiments in hDPP4 transgenic mice
@stevenemassey @quay_dr @Daoyu15 @humblesci @ydeigin @Rcoleptic @Engineer2The 12. Forensic Genomics

8. The ratio of viral to animal reads can show if an animal is a likely host or not.

9. Presence of Pangolin isolate GX/HKU4-GX/2020 in the S. scrofa NGS dataset & similarity to pangolin CoV MjHKU4r-CoV-1 points to a lab construct!

news-medical.net/news/20230622/…
@stevenemassey @quay_dr @Daoyu15 @humblesci @ydeigin @Rcoleptic @Engineer2The 13. How does all this relate to SARS-COV-2?

It is not yet known how SARS-COV-2 acquired its FCS.

This thread shows that SC-2 may have acquired its FCS via cell culture contamination involving GX Pangolin MERS Cov isolates (MjHKU4r-CoV-1) stored & experimented on at WIV in 2019.
@stevenemassey @quay_dr @Daoyu15 @humblesci @ydeigin @Rcoleptic @Engineer2The 14. Why is MjHKU4r-CoV-1 special?

1. FCS are more common in MERS Covs but in the HKU4 group, no such FCS exists.

2. Substitution of KQQR motif at the S1/S2 junction in the bat HKU4 to the RQQR found in MjHKU4r-CoV-1 results in the generation of a minimal consensus FCS (RXXR)! Image
@stevenemassey @quay_dr @Daoyu15 @humblesci @ydeigin @Rcoleptic @Engineer2The 15. Why is MjHKU4r-CoV-1 special? (2)

3. MjHKU4r-CoV-1 Spike is processed by furin

4. FCS enhances viral entry into human cells by 2–3 orders of magnitude compared to bat HKU4

5. Thus, MjHKU4r-CoV-1 Spike has acquired a functioning FCS that conferentry into human cells Image
@stevenemassey @quay_dr @Daoyu15 @humblesci @ydeigin @Rcoleptic @Engineer2The 16. References for the above 3 statements

By guess who?

None other than our our old friend Stuart JD Neil 😂

who tries to interpret the findings in a "Zoonotic" light

See image

Pangolin merbecovirus gets down to (poly)basics

wfmclib.yuntsg.com/official/fwinf…

bookcafe.yuntsg.com/ueditor/jsp/up… Image
@stevenemassey @quay_dr @Daoyu15 @humblesci @ydeigin @Rcoleptic @Engineer2The 17. A Logical Chain & Evidence have now been found

What remains is the question of the exact pathway and experiments that that led to the acquisition of an FCS in Sars-COV-2 in the laboratories of the WIV.

No wonder they refused to share their lab notebooks!
@stevenemassey @quay_dr @Daoyu15 @humblesci @ydeigin @Rcoleptic @Engineer2The 18. A possible pathway (now more likely)

For that, see Bernd Kaina's Paper:

"On the Origin of SARS-CoV-2: Did Cell Culture Experiments Lead to Increased Virulence of the Progenitor Virus for Humans?"

iv.iiarjournals.org/content/35/3/1…
@stevenemassey @quay_dr @Daoyu15 @humblesci @ydeigin @Rcoleptic @Engineer2The 19. Bernd Kaina (1)

1. There is a remarkable identity on amino acid & nucleotide level in & around the FCS between SARS-CoV-2 & a MERS-CoV

2. This supports the hypothesis that the PCS/furin cleavage site was gained by a recombination event(s) involving these virus sequences. Image
@stevenemassey @quay_dr @Daoyu15 @humblesci @ydeigin @Rcoleptic @Engineer2The 20. Bernd Kaina (2)

3. When cells in culture were coinfected with the predecessor of SARS-CoV-2 and another virus strain that contains the PCS/furin cleavage site, the sequence was transferred to the predecessor virus as a result of a recombination event.
@stevenemassey @quay_dr @Daoyu15 @humblesci @ydeigin @Rcoleptic @Engineer2The 21. Bernd Kaina (3)

4. Interestingly, MERS-CoV contains a furin-specific cleavage site, which is very similar to the one found in SARS-CoV-2. As outlined above, there are 6 identical amino acids between position 678 and 687 in SARS-CoV-2 and MERS-CoV.
@stevenemassey @quay_dr @Daoyu15 @humblesci @ydeigin @Rcoleptic @Engineer2The 22. Bernd Kaina (4)

5. Gain of function through the PCS could have happened unintentionally, e.g. after introducing different viruses into a cell to see whether they complement each other functionally (“in trans”), or purposefully in the context of gain-of-function experiments.
@stevenemassey @quay_dr @Daoyu15 @humblesci @ydeigin @Rcoleptic @Engineer2The 23. Bernd Kaina (5)

6. Propagation of the progenitor of SARS-CoV-2 (e.g. RaTG13) together with a MERS-CoV is likely to lead to the selection of a virus that gains functions of both viruses, thus increasing its infection rate in vitro.
@stevenemassey @quay_dr @Daoyu15 @humblesci @ydeigin @Rcoleptic @Engineer2The 24. Bernd Kaina (6)

7. The cells used were equipped with the ACE2 receptor. If these cells also harbored the neuropilin-1 membran protein, selection for a virus showing an even higher virus titer upon propagation in vitro is conceivable.
@stevenemassey @quay_dr @Daoyu15 @humblesci @ydeigin @Rcoleptic @Engineer2The 25. Bernd Kaina (7)

8. It should be noted that cell lines harboring ACE2 together with NRP1 and other desired properties can be generated by routine techniques (transient or stable transfection, lentivirus transduction) and have actually been used for experimental purposes.
@stevenemassey @quay_dr @Daoyu15 @humblesci @ydeigin @Rcoleptic @Engineer2The 26. Summary (1)

The lab hypothesis does not posit that SARS-CoV-2 was genetically engineered on purpose.

The hypothesis tates that SARS-CoV-2 is an unintended byproduct of gain-of-function & cotransfection experiments using human cell lines in vitro. Image
@stevenemassey @quay_dr @Daoyu15 @humblesci @ydeigin @Rcoleptic @Engineer2The 27. Summary (2)

There are many conceivable scenarios how transmission could occur in the lab, e.g. through aerosols during the work or handling of waste. Such lab events could have occurred repeatedly long before December 2019.

They remained undetected with cryptic spread. Image
@stevenemassey @quay_dr @Daoyu15 @humblesci @ydeigin @Rcoleptic @Engineer2The Unroll Pangolin Riddle Solved @threadreaderapp
28. Notes from prior Pangolin Riddle Thread

1. "a virus related to pangolin-CoV appears to have donated the RBD to SARS-CoV-2"

x.com/BillyBostickso…

2. "S gene of pangolin-CoV-2020 may be constructed by fragments from Bat-CoVs ZC45 or ZXC21 & RaTG13"

x.com/BillyBostickso…
29. Holmes on Pangolins at WIV (1)

“Department of State claimed that WIV were working on Pangolins. This is absolute bullshit, it's just made up. Based on zero evidence. Why would you possibly work on a solitary animal with hard keratin scales in a lab?"

30. Holmes on Pangolins at WIV (2) h/t @mentju4

"It’s a completely idiotic suggestion”

Markolin: “I’m not even sure any lab works with pangolins”.

Holmes: “That was clearly put in the report to link that lab with an animal they thought was involved”

31. Coincidences?

Now we must add to the pot MERS Pangolin Cov: MjHKU4r-CoV plus indications of others.

"Isn't it quite strange that 2 of the closest relatives to SARS-COV-2 in different ways, RaTG13 & GX-PV2 were isolated & kept in Chinese Labs?"

32. Comment from @dasher8090

"Pangolins were in the State fact sheet for a reason"

@dasher8090 33. From @virologyanon

Rambaut & Andersen noted that SARS-COV-2 looks like a "convergence" between Pangolin Coronavirus & RaTG13. Billy has now shown that the WIV had all of those viruses & was conducting mutation & recombination experiments on them.

Image
@dasher8090 @virologyanon 34. Also from @virologyanon

Passaging Pangolin coronaviruses and RaTG13, all being done in Wuhan.

Too bad at the time we didn't realise they mutating the MERS-like Furin Cleavage site too - now we do!

Image
@dasher8090 @virologyanon 35. KGA was wondering...

"KGA wondered, did they realise these pango covs had human infective potential and grow them in a lab?

Yes they did, KG!"

Image
@dasher8090 @virologyanon 36. From @CD57227

"Garry figuring out on 10 Feb 2020 that the 'novel' pangolin viruses would have been cultured a long time ago, adding: "Escape.. could happen from a lab and you would PROBABLY never know it."

Image
@dasher8090 @virologyanon @CD57227 37. MERS & SC-2 FCS pathways via @NLink247

"MERS FCS could have rearranged for NRP1 & Semaphorin 3a cleavage motif mimicry from PRSVRSVP which matches most efficient binding peptides for NRP1 & then shifted for ACE2 specificity adopting RRAR which is.."

38. More research on MERS & SARS-COV-2 FCS

SARS-CoV-2 & MERS-CoV Share Furin Site CGG-CGG Genetic Footprint

By Antonio Romeu

Professor of Biochemistry & Molecular Biology.

Abstract

preprints.org/manuscript/202…

PDF

drive.google.com/drive/folders/…

Images show CGGCGG (Asia & Africa) Image
Image
Image
2nd unroll Pangolin Riddle solved @threadreaderapp
Clarification Note

"WIV did have Pangolins in 2019"

That means Pangolin Samples and Viral Isolates, not a zoo full of live pangolins LOL
39. Interesting FCS Update

@gadboit & @daouy15 claim the basic FCS in GX Pangolin MERS Cov isolates (MjHKU4r-CoV-1) held at WIV in 2019 would not have been able to give the FCS to SARS-COV-2.

However @gadboit suggests in this thread another possibility:

@gadboit 40. A big surprise in 2022

"Even with extensive filtering, sample GX/P2V was found to contain 20 reads with exact matches to the SARS-CoV-2 Wuhan-Hu-1 genome"

@gadboit 41. Finding was from a complex paper!

Further analysis of metagenomic datasets containing GD & GX pangolin CoVs



DRASTIC authors focused on refuting the claim of Pangolins as natural hosts but not as Lab "hosts" ;)

@Daoyu15 @stevenemassey @humblesciarxiv.org/pdf/2207.03288
@gadboit @Daoyu15 @stevenemassey @humblesci 42. One thing they did find!

"Lam et al. (2020) sequenced a keratinous pangolin scale and derived the PCoV GD/P2S genome"

"We estimated 99.995% of reads had been filtered out, yet still contamination was detected with 10% of the reads matching the SARS-CoV-2 Wuhan-Hu-1 genome:
@gadboit @Daoyu15 @stevenemassey @humblesci 43. Disturbingly

"The raw sequencing data supporting PCoV MP20 assembly in BioProject PRJCA003816 on NGDC GSA database was embargoed until Sep 2023"

Thus

"No RNA-Seq datasets are available for the GD related PCoV genomes FM45-9, SM44-9, SM79-9 published on GISAID by Xiao K"
@gadboit @Daoyu15 @stevenemassey @humblesci 44. Summary

1. Sample GX/P2V contained 20 reads with exact matches to SARS-CoV-2 Wuhan-Hu-1 genome.

2. @stevenemassey @Daoyu15 @humblesci @ydeigin @quay_dr suggest this was possibly due to contamination

3. @gadboit disagrees with their assessment here

@gadboit @Daoyu15 @stevenemassey @humblesci @ydeigin @quay_dr 45. Review the Arguments Here about the FCS

"Those reads contain one that is a 49nts long, is a perfect match with SARS-CoV-2, and contains the furin cleavage site (FCS)"

Image
@gadboit @Daoyu15 @stevenemassey @humblesci @ydeigin @quay_dr 46. The Key Mutation: C8782T

"As luck would have it the reads that match WH1 *better* than they do P2S happen to contain a site containing a key mutation: C8782T"

Image
@gadboit @Daoyu15 @stevenemassey @humblesci @ydeigin @quay_dr 47. Logic

if this was SC2 contamination then it is in a very early Lineage A variant but it was sequenced in Guangzhou not Wuhan!

Human samples would have had C at 8782, not T

Evidence that the sample was not contaminated and that the FCS was present in the March 2019 samples
@gadboit @Daoyu15 @stevenemassey @humblesci @ydeigin @quay_dr 48. Now for Another Paper 😱

Forensic analysis of novel SARS2r-CoV identified in game animal datasets in China shows evolutionary relationship to Pangolin GX CoV clade and apparent genetic experimentation

assets-eu.researchsquare.com/files/rs-18368…
@gadboit @Daoyu15 @stevenemassey @humblesci @ydeigin @quay_dr 49. Abstract and Conclusion

"The association of this novel CoV with both bat CoV and the Guangxi pangolin CoV (GX PCoV) clades is an important step towards identifying the origin of the GX PCoVs"

researchsquare.com/article/rs-183…Image
@gadboit @Daoyu15 @stevenemassey @humblesci @ydeigin @quay_dr 50. What I recommend

Take time to read the unrolled thread by @gadboit



and feel free to ask questions to me @gadboit @stevenemassey @humblesci @quay_dr or @ydeigin

I believe the Pangolin Samples did contain the SC-2 FCS & were held at WIV in 2019.threadreaderapp.com/thread/1695455…
@gadboit @Daoyu15 @stevenemassey @humblesci @ydeigin @quay_dr 3rd unroll of Pangolin Riddle Solved @threadreaderapp

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