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Alina Chan Profile picture
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3 Dec, 7 tweets, 3 min read
Are these the 8 other SARS viruses from the Mojiang mine? Where can the sequences and metadata be accessed?

The partial RdRp sequence for Ra7896 can be found here: ncbi.nlm.nih.gov/nuccore/MN3126…

Associated with this May 31 preprint, later in Nature Comm: biorxiv.org/content/10.110…
Latinne et al. (EcoHealth, WIV et al.) say "Our host datasets included.. 528 β-CoV sequences (273 new sequences, including 97 new SARSr-CoV sequences (Sarbecovirus) from 31 bat species"

Could be helpful to post the 97 SARSr-CoV sequences in one dataset.
nature.com/articles/s4146…
Also good to note that this manuscript was

Received by Nature Communications on 6 October 2019

Preprinted on bioRxiv on 31 May 2020

Accepted by Nat Comm on 6 July 2020
Scientists @franciscodeasis (not me) have been looking into the Latinne et al. paper since it came out in preprint and have a much better handle on what data was published alongside the paper:
From Latinne et al., "Bat oral and rectal swabs and fecal pellets were collected from 2010 to 2015 in numerous Chinese provinces..." (How did they get Laos bat samples?)

And what about virus samples collected 2015-2019? grantome.com/grant/NIH/R01-…
What did the original draft+supplementary sent to Nature Communications look like? Were any sequences+metadata even shared with the journal or reviewers during the 9-month peer review process?

Preprint posted ~1 month before acceptance.

Scientific publishing needs to change.
Also good to re-point out (initially observed by @franciscodeasis and thanks @emmecola for the reminder) that some of the RaTG13 amplicons from mid-2017 were labeled 7896. Speculation is that 7896's sequence, at least at RdRp, was solved before RaTG13's.

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More from @Ayjchan

Alina Chan Profile picture
4 Dec
"You may disagree with their unconventional approach, but the truth is that these people behave, to all intents and purposes, like a small scientific community: they search and analyze data, they share and discuss their findings and, more importantly, they make discoveries."
Timely piece by @emmecola on how a coalition of twitter users, several anonymous, have been at the front of investigating the origins and sample history of RaTG13 + connection to SARS-like cases among miners from a Yunnan mine full of bats in 2012. mygenomix.medium.com/the-origin-of-…
Their work and fringe (I say this positively) influence on scientists & journalists has led to measurable outcomes. Namely, this @nature addendum, confirming that RaTG13=4991; was seq'ed in 2018, not post-covid; linked to severe respiratory cases in 2012.
nature.com/articles/s4158…
Read 7 tweets
Alina Chan Profile picture
1 Dec
@shingheizhan and I just submitted for peer review our rewritten pangolin CoV manuscript within a mini-review of what we currently know about RaTG13 and the chances of natural spillover in Wuhan. We are hopeful that it gets through this time and will be published in early 2021.
The story about the possible intermediate host and how SARS-CoV-2 spilled over into humans has changed so much over the past year. We were told in Jan that the virus came from wild animals sold at the market. And then in Feb that it was likely pangolins...
All of these trails have fizzled out... leaving no trace of an intermediate host, no clear evidence of natural spillover, while the closest virus relatives are from bats in Yunnan, a thousand miles away from Wuhan city.
Read 5 tweets
Alina Chan Profile picture
1 Dec
Thread breaking down the newest peer-reviewed study suggesting that COVID was on the West Coast in mid December, 2019.
It's not impossible that SARS-CoV-2 arrived in Europe and the US in Dec 2019, but consider that out of 640 throat swabs from Wuhan patients w influenza-like illness, Oct 2019-Jan 2020, only (9) samples in January tested positive for SARS-CoV-2. nature.com/articles/s4156…
Even in the city where cases were detected in Nov 2019, even when only patients with influenza-like illness are considered (not random blood donors), the virus could only be detected in January 2020 patient samples.
Read 4 tweets
Alina Chan Profile picture
30 Nov
Nothing really surprising in the new Wuhan leaked documents shared by CNN, but I find this sobering:

"The documents show health care officials had no comprehension as to the magnitude of the impending disaster."

cnn.com/2020/11/30/asi…
A month before, one of the first whistleblowers was made to sign a letter on Jan 3, 2020 confessing to spreading rumors and violating the law.
"In the future, doctors will be more afraid to issue early warnings when they find signs of infectious diseases." bbc.com/news/world-asi…
The day after Dr. Li signed the letter, a leading Chinese vaccine developer Sinopharm kicked into high gear manufacturing a covid vaccine on Jan 4; 2 weeks before China confirmed human-to-human transmission.
Thanks @norman7177 @dktatlow for sources.
Read 6 tweets
Alina Chan Profile picture
27 Nov
“With publication count highly valued, analysis may also be delayed as teams ‘salami slice’ the underlying results into multiple papers.” 🤣
Been in research for 12+ years and can say that the inability to reproduce a considerable amount of work published even in high IF journals has real costs - to scientists' careers, the research ecosystem, and taxpayers who are ultimately paying for the vast majority of research.
Research publishing can be compared to a game of bluff, where the biggest winners are not necessarily the most honest. But in research, there's no reward for calling someone's bluff, which can likely drag you through years of hell, stalling your own career.
Read 4 tweets
Alina Chan Profile picture
26 Nov
Great article by @sciencecohen
"Not urgently needing the vaccines at home to fight a virus it has largely quashed, (China) is playing a global game.. using the vaccine to promote the diplomacy of foreign policy objectives."
sciencemag.org/news/2020/11/g…
In-depth discussion of China vs the West's vaccine approaches: which can induce broader immunity, is easier to manufacture and distribute, has the risk of antibody-dependent enhancement of covid, and, importantly, can be readily manufactured locally in other countries...
"crucially for China’s vaccine diplomacy, many.. countries have manufacturers that have produced inactivated virus vaccines for decades.. (those) that cannot access vaccines bankrolled by Warp Speed—especially those that hosted China’s.. trials—might have a more secure vaccine.."
Read 5 tweets

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