Alina Chan Profile picture
Oct 25, 2020 36 tweets 19 min read Twitter logo Read on Twitter
Get ready. This is going to be an important thread. Election season will be over soon and hopefully more people will devote some attention to this...

I'm going to walk through a timeline of SARS2-related virus data published in the months after the outbreak. (1/30)
Since the outbreak in late 2019, events have been unfolding at such a fast pace that it is difficult to keep track of what happened and in what order.

I use visualizations of the timeline to follow key events relating to the search for the animal host of SARS2. (2/30) Image
Even today, I still hear people saying that SARS-CoV-2 came from pangolins and a Seafood market in Wuhan. I hope this analysis will help to clear things up. It will refresh us on significant early pandemic events and major publications discussing the origins of the virus (3/30). Image
Notably, many of the key papers describing original data on bat or pangolin coronaviruses closely related to SARS-CoV-2 share co-authors.

The first of these was Liu et al. Viruses (top row). It was reviewed in 3 weeks, published October 24, 2019. (4/30) Image
The first COVID cases were detected in mid-December 2019. Many were linked to the Huanan Seafood market, which was completely sanitized and shut down by Jan 1.

The Chinese lab that first published SARS2's genome was closed for rectification that same day (Jan 12).
(5/30) Image
Jan 20, China finally confirms human-to-human transmission. Same day, WIV's paper is sent to @nature describing an unattributed bat virus 96% identical to SARS2.

Jan 22, China says the virus likely came from animals sold at the Seafood market.

Jan 23, WIV paper on bioRxiv. Image
At the same time, on Jan 22, Liu et al. re-uploaded their September 2019 pangolin virus data onto @NCBI Why? Are the two datasets identical?

Jan 31, in a non-public meeting, China informs @OIEAnimalHealth that none of the market animal samples were positive for the virus. (7/30) Image
This is where it gets even more interesting.

Within weeks, 4 manuscripts describing a pangolin virus with a similar spike RBD to SARS2 were submitted to journals (2 went to @nature); 3 were preprinted @biorxivpreprint the same day (Feb 20).

Remember the shared authors. (8/30) Image
Notably, all 4 manuscripts relied heavily or solely on the Liu et al. Viruses paper. Xiao et al. @nature renamed samples, failed to attribute them properly, produced a profile that did not match any sample in their paper. Liu et al. @PLOSPathogens is still missing data. (9/30) Image
The public release of all 4 manuscripts on @biorxivpreprint between Feb 18-20 sent the public into a frenzy, speculating that pangolins were the intermediate hosts who had given SARS2 to humans in a Wuhan wet market - particularly based on the prevailing public info at the time. Image
Soon, another preprint describing a closely related bat virus, RmYN02, and a @NatureMedicine correspondence "The proximal origins of SARS-CoV-2" were published. These both share an author with Lam et al. @nature and both proposed that SARS2's origins are natural. (11/30) Image
The manuscripts each passed journal+peer review in 2.5 months max (the fastest took only 9 days @nature).

However, none of the papers shared amplicon data. Some didn't even share raw data. It was impossible for scientists to independently assemble the published genomes. (12/30) Image
May 19, amplicon data for RaTG13, the most closely related virus genome to SARS2, was quietly deposited onto @NCBI without explanation by Zhou et al. @nature This data revealed that the sample had been sequenced in 2017/2018 and not post-COVID as the paper suggested... (13/30) Image
Furthermore, the data do not match the original RaTG13 published genome. No explanation for how this could've happened. Or, more importantly, which private virus database the sequences and data had been stored in for years, and if there are other SARS viruses we don't know about.
Meanwhile, studies were pointing out that there was zero evidence of SARS2 spillover from animals into humans at the Wuhan Seafood market. By May 25, the Chinese CDC director announced that the market may have been a victim and not the site of spillover as they first thought. Image
June 22, a new pangolin virus preprint appears. On the same day, data from a new pangolin sample was added to the already published Xiao et al. @nature bioproject, but the sample was not described in any text/figure of the paper. Its profile instead resembled one in the preprint. Image
@nature had been notified in May that the core data in Xiao et al.'s paper was (and still is) not accurately reported. The mysterious sample profile in their extended fig 4 is still unaccounted for, even with the addition of the new sample. (17/30) Image
The story gets more complicated by this new preprint Li et al. @biorxivpreprint because it shares author(s) with Proximal Origins @NatureMedicine, Natural Insertions/RmYN02 @CurrentBiology, both pangolin CoV @nature papers, and thereby the original Liu et al. Viruses. (18/30) Image
On July 7, @shingheizhan and I preprinted our finding that the Guangdong pangolin virus genomes by the 4 papers primarily used data/samples from the same batch of pangolins, and that key data was inaccurately reported by Xiao @nature and Liu @PLOSPathogens… Image
We submitted our manuscript to a journal in May and tweeted about these findings to raise awareness about these problems. After 21 weeks in review, we received a very disappointing decision from the editor. However, we have updated our preprint. Separate thread to come. (20/30)
Separately, on July 24, the WIV confirmed suspicions that RaTG13 was not a novel virus, but actually had been published in 2016 (then named btCoV/4991) and that the sample was sequenced and depleted in 2018 (not post-COVID). Nothing left for independent verification. (21/30) Image
More troublingly, this raised questions about why RaTG13 had been inaccurately reported+unattributed in Zhou et al. @nature and even in the recent review by Shi in @NatureRevMicro. As well as its connections to mysterious SARS-like cases in 2012 investigated by top Chinese labs. Image
By September, scientists were pointing out the mismatched RaTG13 published genome vs the raw+amplicon data. Oct 13, the RaTG13 genome was quietly updated on @NCBI again no explanation by Zhou et al. @nature -how the mismatch occurred, how the sample was processed exactly. (23/30) Image
In parallel, in August, @CurrentBiology was notified about the missing raw+amplicon data for RmYN02. Thankfully, they made the authors share the raw data on a secure site, but the amplicon data is still missing; the published genome cannot be independently assembled. (24/30) Image
So, just putting all of these events back on the timeline. It's very frustrating that critical information on SARS2 origins is coming out almost on a need-to-know basis. And we have no idea what's going on behind the scenes among the journals, authors, peer reviewers. (25/30) Image
@shingheizhan and I have just spent 21+ weeks in review for 1 manuscript pointing out the major inaccuracies in key papers describing the Guangdong pangolin virus with a SARS2-like RBD. There's a lot of stuff going on that I think the public needs to demand to hear about. (26/30)
Where are we today?

The published GD pangolin CoV genome and RmYN02 genome still cannot be independently assembled because of data not shared with the public. @nature @PLOSPathogens @CurrentBiology

Isn't it important to get this data from the authors? (27/30) Image
We still don't understand how the original RaTG13 genome did not match the raw+amplicon data. More importantly, why RaTG13 sample history was inaccurately reported by Zhou et al. @nature and why a correction to the paper hasn't been issued despite public admission RaTG13=4991.
I welcome public peer review by non-anonymous experts & fact-checking of the analysis above. After collecting your valuable feedback, I will edit the images into an animated gif, and prepare to write a short article about what we know and don't know about SARS-CoV-2 origins.
Popular request: top points.

1. Public has little idea what happened/is happening behind the scenes with journals x authors of SARS2rCoV papers.

2. The closest related virus genomes to SARS2 cannot be independently assembled due to missing data/have unexplained indiscrepancies.
More questions coming in.

1. Is this a giant conspiracy.

2. Does this mean SARS2 was from a lab?
We don't know. There's no sign of an independent investigation of origins right now. Plus, so much time has passed.

3. Is SARS2 an intentionally released bioweapon?
Also, several people asking me about what I think about Dr. Yan's reports. So I will link my threads:

1st report

2nd report
I'll add to this, in case those threads tldr, that I don't doubt Dr. Yan's qualifications. I believe who she says she is - she has years of virology, scientific+medical training, one of the earliest to work on SARS2. I believe her about the cover-up on human-to-human transmission
I support whistleblowers. That being said, I will not automatically endorse Yan's reports. I do think there are massive problems identified by these reports that should be addressed by the scientific community. But, these are overshadowed by biased claims in the reports.
Next day update: I'm getting quite a bit of emails and tweets from people I don't know with links to papers and pdfs.

I apologize but I'm not going to click on any of these links or reply to these emails. It's not personal. I just cannot take the risk right now. Thank you.

• • •

Missing some Tweet in this thread? You can try to force a refresh

Keep Current with Alina Chan

Alina Chan Profile picture

Stay in touch and get notified when new unrolls are available from this author!

Read all threads

This Thread may be Removed Anytime!


Twitter may remove this content at anytime! Save it as PDF for later use!

Try unrolling a thread yourself!

how to unroll video
  1. Follow @ThreadReaderApp to mention us!

  2. From a Twitter thread mention us with a keyword "unroll"
@threadreaderapp unroll

Practice here first or read more on our help page!

More from @Ayjchan

Jul 23
Many experts initially expected the 2019 outbreak to follow the same trajectory as the 2003 SARS epidemic.

If it had been made public that the virus plausibly came from a lab, I believe this would've made decisionmakers rethink their assumptions about transmissibility in humans.
By the time significant differences were noticed between the 2019 pandemic virus and the 2003 SARS virus, it was too late.

No infected animals were reportedly found at the market, other markets, any farms, or anywhere along the supply chain.
To quote one Proximal Origin author:

"the Wuhan virus is beautifully adapted to human transmission but we have no trace of that evolutionary history in nature... I am struck by how differently this virus is behaving from SARS."
Read 7 tweets
Jul 20
The Proximal Origin authors have lost the moral high ground. In their private discussions of a lab #OriginOfCovid they mocked virus hunters for not being able to predict outbreaks of their own making and steered journalists away from asking hard questions about a lab leak.

Kristian Andersen said that performing gain of function experiments in BSL3 or less is completely nuts and that he wasn’t sure that the knowledge gained from these types of exceptionally dangerous experiments is at all actionable.

“It only takes one mistake.” Image
They knew that GOF proponents they had talked with were asking for specific evidence proving a lab #OriginOfCovid but this was impossible to obtain except for the most simple scenario where someone used a published construct.
Read 19 tweets
Jul 12
Longer email and slack conversations can be extracted from the select subcommittee's report on Proximal Origin.
Feb 2, KA: "[RF & CD] are much too conflicted to think about this issue straight - to them, the hypothesis of accidental lab escape is so unlikely and not something hey want to consider. The main issue is that accidental escape is in fact highly likely."

KA: "I'm all for GOF experiments... however performing these in BSL-3 (or less) is just completely nuts!"

On mammal-transmissible flu study, "I'm not sure that type of knowledge is at all actionable, while, of course, being exceptionally dangerous. It only takes one mistake."
Read 11 tweets
Jul 7
Chinese CDC director confirmed that early covid cases had been identified with a bias toward the market.

In contrast, people seeking help via social media in Wuhan, Dec 20-Jan 18, were predominantly in the district of the Wuhan Institute of Virology.…
I'm not saying that you can tell from the early case home addresses or from the location of help seekers how the virus first got into people.

But if someone believes you can do this, then they should acknowledge the spatial data pointing to the Wuhan lab.
Either way, none of this is dispositive or incontrovertible.

To definitively find the #OriginOfCovid we have to track down the very earliest cases and pin down their exposures to the virus - whether in the lab or an infected animal in the market.
Read 12 tweets
Jun 30
I would also like to know if @WHO @mvankerkhove can shed some light on this engagement with NIAID senior scientific advisor and Proximal Origin authors bashing scientists like myself who are asking for an investigation of plausible lab #OriginOfCovid
@WHO @mvankerkhove The Proximal Origin authors clearly have a direct line into the @WHO
@WHO @mvankerkhove And the scientist who convened the Proximal Origin authors and advised the drafting of Proximal Origin is now the @WHO chief scientist.
Read 4 tweets
Jun 29
Emails from Sep 2021 between:
1⃣NIH (David Morens, advisor to Anthony Fauci)
2⃣EcoHealth Alliance (Peter Daszak)
3⃣Proximal Origin & friends (Kristian Andersen, Ed Holmes, Bob Garry)

Morens wrote: "Tony doesn’t want his fingerprints on origin stories."

Daszak wrote that the rules were "meant for pathogens that occur in humans and might be made more dangerous" so it didn't apply to bat viruses. His belief seemed to be that creating chimera in the lab was less risky than isolating new viruses. Debatable.…
Kristian Andersen tells Peter Daszak the recombinant human pathogen MERS work at the WIV might be considered gain of function. Daszak emails back saying they "didn't do this work".

Turns out they did do the work. It's in their late report to the NIH.
Read 16 tweets

Did Thread Reader help you today?

Support us! We are indie developers!

This site is made by just two indie developers on a laptop doing marketing, support and development! Read more about the story.

Become a Premium Member ($3/month or $30/year) and get exclusive features!

Become Premium

Don't want to be a Premium member but still want to support us?

Make a small donation by buying us coffee ($5) or help with server cost ($10)

Donate via Paypal

Or Donate anonymously using crypto!


0xfe58350B80634f60Fa6Dc149a72b4DFbc17D341E copy


3ATGMxNzCUFzxpMCHL5sWSt4DVtS8UqXpi copy

Thank you for your support!

Follow Us on Twitter!