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Alina Chan Profile picture
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26 Feb, 5 tweets, 3 min read
To get a sense of how slowly investigations into the origins of covid-19 / SARS2 are going...

In the case of SARS1 (2002-2004), virus emerged late in the year 2002.

1st virus isolated in March 2003. 1st genome sequence in April 2003.

Market animal sources found in May 2003.
Oct 2003, it was reported that the animal trading community had previously undetected exposure to SARS virus(es).

In other words, SARS1 was found to have spilled over in a place where animal traders are exposed to similar viruses.

cdc.gov/mmwr/preview/m…
When SARS1 emerged again in late 2003, the tracking of the spillover source was even faster.

Patient (a waitress) diagnosed on Jan 2, 2004.

In 2 days, samples had been collected from all palm civets and employees at the restaurant. Several samples SARS+

ncbi.nlm.nih.gov/pmc/articles/P…
By Jan 5, 2004, the outbreak had been traced to a market:
"The virus was identified in all 91 palm civets and 15 raccoon dogs of animal market origin.. not in.. later sampled.. 25 farms.. claimed to be the source of traded animals."
pubmed.ncbi.nlm.nih.gov/15921605/
ncbi.nlm.nih.gov/pmc/articles/P…
It helps to compare the technology available in 2003 vs in 2019.

2003: had to first culture the virus, then clone cDNA products for individual sequencing (Marra 2003 Science)

2019: can just next-gen sequence the sample (Zhou 2020 Nature) - a few days to full genome.

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More from @Ayjchan

Alina Chan Profile picture
27 Feb
Starting to wonder how many virus samples are sitting in freezers waiting to be sequenced.

The newest pangolin CoV in GISAID (EPI_ISL_610156) was collected in Yunnan in 2017. Someone implied that this was proof of the 2019 Guangdong pangolin CoV, but it's quite different...
The Yunnan pangolin CoV sequence is full of gaps, missing front half of the Spike, no RBD to even compare with the SARS2-like RBD in the Guangdong pangolin CoV.

Not sure why anyone would think this Yunnan pangolin CoV is useful to verifying the history of the GD pangolin CoV.
Meanwhile, the Guangdong pangolin CoV authors who haven't provided any of the novel raw data mentioned in their May 2020 @PLOSPathogens paper just released more short sequence fragments for another paper?
ncbi.nlm.nih.gov/popset?DbFrom=…
Read 7 tweets
Alina Chan Profile picture
26 Feb
“scientists expressed surprise and even disbelief that the further investigations, into both the first patient's contact history and the supply chain to the Huanan market that the WHO sought, had apparently not already been performed by China.” cnn.com/2021/02/21/chi…
“specialist Daniel Lucey.. said it was “frankly implausible” that such testing had not been done. “My question is why would it not have been done? It was known to be necessary and it’s in China’s scientific.. public health.. national security interest””
scmp.com/news/china/sci…
This would be like if in Stranger Things, the protagonists all neglected to investigate the local National Laboratory while searching for the inter-dimensional gateway (source of spillover).
Read 4 tweets
Alina Chan Profile picture
26 Feb
Am I getting this right? The @WHO convened team heard from an index case that there was a 2nd market but because the meeting ended, they didn’t get details or even the name of the market.

“On the next episode of CSI Wuhan...”
wsj.com/articles/in-hu…
Also, before the WHO-convened team went to Wuhan, Chinese scientists had already tested 10,000s of animal samples including from around Wuhan city and Hubei province - all negative for SARS2. Can the team access the data in higher resolution? Which markets and farms were checked?
A timeline of when results were known would also be exceedingly helpful. The @WSJ reported on this in May 2020, eg OIE was informed on Jan 31, 2020 that no animals at the Huanan market tested positive for SARS2. wsj.com/articles/china…
Read 4 tweets
Alina Chan Profile picture
25 Feb
Feb 9, we heard from WHO-convened team (which is 50% scientists in China, 50% international) they were going to stop looking into "extremely unlikely" lab origins & start investigating #PopsicleOrigins

One team member said this decision was to "respect" the Chinese counterparts.
Feb 22, one of WHO-convened team members says the COVID-19 virus could've come from Thailand, even naming one market.

DESPITE closest relatives to SARS-CoV-2 being from China

DESPITE the virus in Thailand not even using the same human receptor 🤯

bangkokpost.com/thailand/gener…
Jan 2020 China said the virus likely came from wild animals sold at the Wuhan seafood market. May 2020 they said the market was just a later cluster, not the origin.

Since then, they've suggested that covid-19 was imported into China through cold chain.
Read 7 tweets
Alina Chan Profile picture
24 Feb
People have been asking me about this article by previous Secretary of State Mike Pompeo and Miles Yu in @WSJ

How much of this is objective? Or novel? Could SARS-CoV-2 / COVID-19 really have come from a lab in Wuhan?

What do we really know, publicly?
wsj.com/articles/china…
On Jan 15, 2021, the previous US State Department released this Facts Sheet on the origins of COVID-19 raising concerns about SARS + other pathogen research at the WIV.

However, it was swiftly archived by the new administration.

2017-2021.state.gov/fact-sheet-act…
On @FaceTheNation ex-Deputy National Security Adviser Matt Pottinger said that this had been "scrubbed by every department within every bureau within the State Department, was looked at very carefully by the NSC staff, intelligence officers, HHS"
cbsnews.com/video/former-d…
Read 12 tweets
Alina Chan Profile picture
22 Feb
One fact that I think many scientists and members of the public are not widely aware of is that the original SARS virus - back when it was the only SARS virus known to man - escaped from labs not once but 4 times.

2 of those times from a top Beijing lab.

genomebiology.biomedcentral.com/articles/10.11…
For those lab escapes of SARS1, "once the alarm was raised about the cases, over 1000 of their close contacts were isolated very quickly"

But would this have stopped a virus like SARS2 that can spread asymptomatically with up to 2 weeks incubation time?
ncbi.nlm.nih.gov/pmc/articles/P…
In 2004, SARS was the only SARS virus studied in labs - 4 lab escapes.

Fast forward to 2019, there are several dozens (likely 100s) of SARS-like viruses sampled by labs.

After covid, a whole bunch of SARS2-like viruses collected in the past get published.
Read 10 tweets

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