Alina Chan Profile picture
Oct 25, 2020 36 tweets 19 min read Read on X
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 biorxiv.org/content/10.110… 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.
No?

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?
Unlikely!
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.

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More from @Ayjchan

Mar 13
I encourage experts who have insisted on a natural origin of Covid-19 to gracefully change their public stance instead of doubling down on the threadbare evidence for the wet market hypothesis.

You could acknowledge that you initially trusted your colleagues in China/US to tell the truth. But time and time again over the past 5 years, it has been shown that they withheld critical evidence from you and the public:
1⃣The 2018 Defuse proposal
2⃣Low biosafety standards for experiments where live viruses are produced and used in human cell infection studies
3⃣Risky pathogen experiments and surprising gain of function
4⃣Missing pathogen sample database, viruses discovered after 2015 largely not shared with US collaborators
5⃣Closest virus relative that we know of was collected from a mine where people died from suspected SARS-like virus infection

The studies published last month where Wuhan scientists experimented with potentially dangerous pathogens at low biosafety opened your eyes to the level of reckless ambition in their research.

Given these betrayals, it is fully within reason to retract your trust and re-evaluate all the available evidence. Those of you who have access to intelligence could say that the non-public evidence has cast a new light on the public evidence and strengthens the case for a lab origin of Covid-19.

This is better than continuing to argue that you somehow know all the viruses in the Wuhan lab's collection and somehow know they didn't follow through on their 2018 plans to put furin cleavage sites into SARS-like viruses and study these at low biosafety exactly like they said they would.
For those experts who haven't even looked at the Defuse proposal and its drafts, the Wuhan-US scientists clearly said they were interested in furin cleavage sites at the spike S1/S2 junction, and would insert these into novel SARS-like viruses in the lab (not closely related to the 2003 SARS virus as that would be dangerous). They would test the ability of these SARS-like viruses with inserted cleavage sites to infect human cells and cause pathogenesis in vivo.

The Wuhan lab was regularly synthesizing novel coronavirus genomes without leaving any sign of lab manipulation. They used a protocol with trypsin-supplemented media to retain cleavage sites in the viruses. They did much of the work, including infection experiments in human cells, at BSL-2. Their US collaborator Ralph Baric has repeatedly criticized them for doing the work at low biosafety.

h/t @emilyakopp for FOIA'ing the Defuse proposal drafts.Image
Image
Some virologists may argue that the furin cleavage site in SARS-CoV-2 doesn't look canonical. You should read the citation in the Defuse draft for the computational model used to predict furin cleavage sites. The paper says it doesn't rely on the canonical motif and instead looks at a 20-residue sequence to make its predictions. The PRRAR motif exists in a feline coronavirus, MERS has a PRXXR S1/S2 furin cleavage site, and the RRXR motif is a functional furin cleavage site in numerous other proteins.
Read 13 tweets
Mar 12
According to Zeit Online, German Chancellery consulted with US Director of National Intelligence in 2023, who said there was nothing to the lab leak hypothesis.

They doubted "Eierköpfe" (egghead) scientists in intelligence knew better than leading virologists around the world.
In the US, something similar was happening where scientists in intelligence agencies also assessed a likely lab origin of Covid but were sidelined.

"The dominant view within the intelligence community was clear when... the director of national intelligence, and a couple of her senior analysts, briefed Biden... concluded with “low confidence” that Covid-19 had emerged when the virus leapt from an animal to a human."
wsj.com/politics/natio…
In both cases, government leaders favored the opinions of leading virologists over the scientists working in intelligence. Even though some of the leading virologists were public advocates and funders of "gain-of-function" research of concern with pathogens.
Read 4 tweets
Mar 12
German intelligence now assesses a 80-95% likelihood of a lab origin of Covid-19. Image
Image
Read 4 tweets
Mar 9
I am not 100% convinced Covid came from a lab. I still think there is a small chance the virus emerged in Wuhan without the help of research activities. However, this would mean:

1⃣ The Wuhan-US scientists' entire framework about the spillover risks of SARS-like viruses, building on research and data collected over more than a decade, was incorrect.

2⃣ A highly transmissible, super stealthy virus well adapted for causing uncontrollable outbreaks in multiple animal species left zero trace of its origin in the wildlife or fur farms of China/SE Asia after emerging in only Wuhan out of 1000s of other populous cities.

3⃣ Out of all possible viruses to cause a pandemic and all times for a pandemic to occur, it was an unprecedented SARS-like virus with a novel furin cleavage site, matching the description of a 2018 US-Wuhan research proposal, emerging in Wuhan where scientists worked with such viruses at low biosafety, less than 2 years after said proposal was drafted.

It's not impossible that leading experts were completely mistaken about the exceedingly low odds of such viruses emerging in Wuhan.

It's not impossible that, in 2019, nature churned out a virus matching the scientists' 2018 research plans and that virus emerged in only Wuhan of all places.

But you'd have to be very motivated to believe Covid-19 emerged naturally.
We are unlikely to reach 100% certainty unless a whistleblower appears or the Chinese authorities one day assess that it is in their interest to share the truth.

I am still hopeful that this will happen one day. I believe in human courage.
Before that day, there are several routes of investigation that remain to be explored by the US gov.

Conducting a rigorous, credible investigation of Covid origins can unearth more key evidence while also informing the implementation of new measures to prevent lab pandemics.
Read 5 tweets
Mar 8
Top journals have the power to set global biosafety standards.

It's a problem that they do not see this as their moral responsibility. By publishing & celebrating risky research done at questionable biosafety, they incentivize the 'work fast break things' model of research.
I've given up on journals taking the initiative to be responsible members of the scientific community.

It is up to the U.S. government to tell them to behave responsibly or do business elsewhere.
I would love to be corrected if any top journal can show us that fostering a culture of accountability, scientific integrity, and 'do no harm' is one of their measurable goals as an organization & a strict criteria for decision-making regarding what research/groups to publish.
Read 6 tweets
Mar 2
Dear @NSAGov I've just google searched several human transmissible viruses with the aim of understanding how many are not governed by the Federal Select Agents Program and can be used in gain-of-function research by privately funded groups.

I am not doing anything nefarious 🙏
@NSAGov The answer is there are a lot of human transmissible viruses that are not governed by the Federal Select Agents Program and can be used in gain-of-function research by privately funded groups.
@NSAGov Novel SARS-like and MERS-like viruses are not select agents. Meaning scientists in the US can bring these to their labs in major cities and enhance them without informing the authorities.

At any biosafety level they see fit.
Read 5 tweets

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