Thread by @Ayjchan

More SARS virus research theses unearthed by @TheSeeker268 and analyzed by @franciscodeasis

This time from Shi Zhengli's lab at the Wuhan Institute of Virology (WIV). Pointing to more SARS2-like viruses in their possession.

https://twitter.com/TheSeeker268/status/1392575191763472388

Highlights: one WIV thesis from 2014 acknowledges the cases of the Mojiang miners, saying that they suspected a bat virus infection!

They also collected and were testing more patient sera than acknowledged in their @Nature addendum in Nov 2020.

https://twitter.com/TheSeeker268/status/1392575204040212488

Linfa Wang, long time collaborator of Shi and Daszak, was thanked in the thesis for his guidance on this Master's project: "再次，要感谢澳大利亚动物健康研究室的王林发老师对我硕士期间所做课题的指导。"

Did Wang know about the miners?

https://twitter.com/TheSeeker268/status/1392575233274482688

Was this @NatGeo June 2020 quote by Wang a reference to the 3 Mojiang miners who had died?

"In Wuhan, if three people died and it was controlled, would we know it? No. This is happening all the time, it's just in remote villages where people die."
nationalgeographic.com/science/articl…

Confusingly, the thesis described its samples as having been collected in 2012: "2012年8月和9月在云南墨江分别采集了77份和93份样品。"

Ra4991 aka RaTG13 was apparently, according to the thesis, one of these samples.

I thought the WIV said it was collected in 2013?

Another thesis, from June 2019, describes an entirely new lineage of SARS viruses under study at the WIV - the lineage that SARS2 is in - and you can see from the figure that there were 9 in total: Ra4991 and eight others.

The author of the 2019 thesis publishes on the same project (paper submitted Nov 2018, published Feb 2019). Spot the difference.
pubmed.ncbi.nlm.nih.gov/30735813/

Covid-19 rolled around. WIV published their 1st paper in @nature Brought up RaTG13 without explaining the link to SARS-like cases in 2012, that they had sequenced its genome in 2018, and that there are a whopping 8 other viruses in this SARS2 lineage.
nature.com/articles/s4158…

It took the WIV team all the way until Nov 2020 before they acknowledged all these omissions but still did not disclose the ID of these 8 other SARS viruses from the deadly mine or their sequences...

@nature you might need an addendum to the addendum.

nature.com/articles/s4158…

Some may ask, why did they even reveal the presence of these 8 SARS viruses from the mine? Especially if they hadn't disclosed it in the 2019 Infection, Genetics and Evolution paper. That's because of another paper in the Nature family:
nature.com/articles/s4146…

Internet sleuths (some are scientists) had picked up on a "7896" in the RaTG13 sequencing data and mapped it onto a sequence uploaded in connection to the Latinne et al. EcoHealth-WIV 2020 paper.

Read more here about their analysis:
researchgate.net/publication/35…

From @BillyBostickson's lab:
"Latinne et al. (2020) was initially published as a pre-print on Biorxiv on May 31, 2020, despite being submitted long before to Nature for review on October 6 2019. The Fasta files were... processed by NCBI on 07-Nov-19..."

I want to emphasize the labor of these detectives. The data was hidden in the supplementary, after which you had to go through a ridiculous number of sequence IDs to check for these SARS2-related sequences that the paper didn't even mention.
static-content.springer.com/esm/art%3A10.1…

I re-read the Aug 2020 paper again just to be sure. No mention of the new bunch of close relatives to SARS-CoV-2. No attention drawn to these new sequences.

Why would you do this?
nature.com/articles/s4146…

Last 3 senior authors: Linfa Wang, Zhengli Shi, and Peter Daszak.

Honestly, I'm very curious to see the first version of this Latinne et al. manuscript that was sent to @NatureComms and the peer review that it went through.

A preprint was posted in May 2020, the paper was submitted Oct 2019 and published in August 2020.

In this mine, where people had sickened with severe respiratory disease, 64% of the bat samples had many types of coronavirus in it. "所获得的N基因、S基因片段来自多种冠状病毒。"

Yet, the paper doesn't highlight the sequences they got from this virus mine.

https://twitter.com/TheSeeker268/status/1392575226345447427

I'm not super sure these scientists understand the mandate of their virus hunting program.

When you find clusters of mysterious illnesses and find potentially concerning viruses from the location, shouldn't it be both urgent and important to immediately publish those findings?

At the bare minimum, when you report these findings, the sample histories, sequences, and data should be accurately described and made publicly accessible in a timely fashion.

Just in case you're wondering, yes, this is the mine that several teams of journalists have been trying to visit but get blocked each time. One of those times, the journalists were told that there were wild elephants in the area 🦇🦇🦇🐘🦇🦇🦇🦇🦇🦇

https://twitter.com/TheSeeker268/status/1370222502270562308

That's all I have to say for now, but I would like to give a big shoutout to @franciscodeasis for his careful analysis (still ongoing) & @TheSeeker268 for his magical powers of unearthing these theses, and the internet sleuths who continue to investigate.

https://twitter.com/franciscodeasis/status/1392600443856080898?s=20

More interesting tidbits from @franciscodeasis -confirmation that the Latinne et al. data had been processed by Genbank in early November 2019 but changes had been made in April and May 2020 after the pandemic was well under way. What were these changes?

https://twitter.com/franciscodeasis/status/1363646305235533825

It's so ridiculous that finding out more about these papers describing some of the closest relatives to SARS-CoV-2 - providing clues as to its origin - has to involve a suite of internet sleuths and science hobbyists working OT, as well as FOIA requests to the US-based NCBI.

People in charge, please convene a proper investigation with the authority to immediately obtain these types of information.

Are you possibly waiting for an even larger and more devastating pandemic before you'll get serious about finding its origin?

More on this developing story h/t @DecrolyE @Biol4Ever
One of the top priority SARS viruses, Rs8561_Guangdong chosen for full genome sequencing is very distinct from the 2003 SARS virus, although both are in Lineage 1; Ra4991_Yunnan is Lineage 4.

https://twitter.com/TheSeeker268/status/1392575296646180868

If the work from the WIV had all been published and made available on @NCBI GenBank like Dr Shi has said before, then why do we not know about Rs8561 except through a 2019 masters thesis?

What is this novel SARS virus chosen for full genome sequencing?

This too: looks like WIV found an exceedingly close match to 2003 SARS but we don’t have access to the full genome of Rs5725_Yunnan.

It’s not strange for labs to sit on new data, but a SARS(2) pandemic might be a good time to share these data to put other scientists at ease.

https://twitter.com/babarlelephant/status/1392867188806139904

Under current circumstances, each one of these super novel SARS virus genomes may be able to be its own standalone high impact paper. It certainly worked for the single Guangdong pangolin SARS-like virus. In fact, it resulted in at least 4 research papers in early 2020.