Alina Chan Profile picture
Scientist-turned-detective | Postdoc at the Broad Institute of MIT and Harvard | my opinions are my own 🇨🇦🧬🐉
Jeremy White Profile picture Medical Science and Technology «Спутник V» Profile picture Russian bot Profile picture Angelica, MD, PhD Profile picture NLW Profile picture 23 added to My Authors
5 Mar
“based on what we know so far.. the W.H.O. investigation appears to be biased, skewed, and insufficient.. without full transparency and access to the primary data and records, we cannot understand the basis for any of the comments issued so far” nytimes.com/2021/03/04/hea…
... as @R_H_Ebright said, the open letter was released in anticipation of an interim report from the WHO-convened covid-19 origins study team. Our letter was communicated to high levels of @WHO on Tuesday, and we only heard this morning that no interim report is coming after all.
We can talk about the full report when it comes out but should not wait to call for global efforts as @FilippaLentzos described, possibly involving the U.N. General Assembly where all nations are represented and can vote on whether to formally investigate #OriginsofCOVID
Read 11 tweets
4 Mar
The WHO-convened covid-19 origins study group is scrapping their overdue interim report amid "tensions between Beijing and Washington over the investigation and an appeal from one international group of scientists for a new probe."
wsj.com/articles/who-i…
Many thanks to the experts & scientists who organized the open letter which is the basis of the @WSJ news story.

The letter describes limitations of the WHO-convened global study and what a credible investigation into COVID-19 origins should look like. s.wsj.net/public/resourc…
And also thanks to @WSJ @betswrites @drewhinshaw @JNBPage for staying on this story & doggedly reporting on the origins of covid-19.

I really think this is just the beginning. It is unlikely that the world will just move on and not seek answers to where this pandemic came from.
Read 11 tweets
3 Mar
Are there any more densely populated cities with extremely high traffic international airports that we can build more BSL4 labs in?
Just making sure that lab personnel will be able to get from the BSL4 to the nearest very highly visited food village in ~20min via MRT (metro). Image
And the world famous Changi airport in ~25min drive. One of the world's busiest airports by international passenger and cargo traffic... Image
Read 4 tweets
2 Mar
FYI journalists reporting on the @WHO convened COVID-19 origins collaborative process of discovery.

@DrTedros said it is not a WHO study or investigation.

It is an independent study by predominantly non-WHO experts. ~Half of the team is unidentified.
who.int/publications/m…
The WHO-convened team had to work with Chinese counterparts (half of the team) in a collaborative process; they did not have investigatory powers to look into COVID-19 origin hypotheses that their hosts did not want them looking into.
This was reinforced by the leader of the WHO-convened team in a recent @ScienceMagazine interview: sciencemag.org/news/2021/02/p…
Read 16 tweets
1 Mar
This is a good piece that communicates some of the major misunderstandings held by scientists and experts exploring the origins of SARS2 / COVID-19.
The first major misunderstanding:

Some experts keep saying it took a decade to confirm that SARS1 came from bats.

But in 2003 and 2004, the animal sources of SARS1 were found within 2 months and 1 week, respectively.
So I think these top experts studying the origins are very very confused.

They’re looking for the ancestral origins of SARS2 in bats.

But finding the proximal origins of the virus shouldn’t take a decade.
Read 20 tweets
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 11 tweets
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
26 Feb
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…
Read 5 tweets
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
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
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
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
21 Feb
Before the WHO-convened global study on the #OriginsofCovid releases their interim report this week (maybe), I think it's useful to explain to the public where all the evidence lies right now across the 4 hypotheses presented by the origins team
who.int/publications/m…
For the sake of simplicity, hypotheses 1 and 2 can be combined into scenario A, which includes virus transmission from the animal reservoir (most likely bats) directly into humans or through an intermediary animal host that is more closely related to humans.
The WHO-convened team stated that cold chain supply (scenario F) is an #originsofcovid hypothesis deserving of follow-up.
Importantly @Peterfoodsafety later clarified they are only considering within-China cold chain food trade, not from outside China.
Read 25 tweets
19 Feb
“Chinese authorities declined to give the WHO team raw data on these cases and potential earlier ones”

Data they saw “could possibly indicate infections as far back as September, said Marion Koopmans, a Dutch virologist on the WHO team.” wsj.com/articles/covid…
🌟 by @LawrenceGostin
“Sovereign states will almost certainly resist IPPPR proposals to empower the WHO to enter their territory and gain access to full information.. (eg) inspectorate system like the ones currently in nuclear nonproliferation treaties.”
jamanetwork.com/channels/healt…
The @WHO origins study shows us serious problems in pandemic reporting & tracking. Tho much data exists & more could’ve been found a yr ago, no world organization was granted the power to access and collect such data.

As a result, the world doesn’t even know when covid started.
Read 5 tweets
18 Feb
We can credit the @WHO coordinated exploration with some things: They got into China after 1 year. They got to see what their Chinese counterparts had prepared for them, itinerary and reports. They got to see what their Chinese counterparts would not share with them or answer...
What I would like is if the team can carefully lay out: What they asked. What answers/data they were given or not given. Their hourly itinerary, who was in attendance at each event/meeting, if there was voting (and if there were non-unanimous votes; just numbers, not identity)...
I understand that a summary, full report & pressers are coming but these have to be signed off by ALL members including 50% of the team who are scientists in China.

Can journalists talk to non-Chinese teammates w/o disclosing their identities to get a handle on what happened?
Read 9 tweets
18 Feb
Some scientists expected this day would come but somehow it's still annoying that it's gotten to a stage where some individuals are infected by 2 or more separate people/events, sometimes resulting in recombination between different SARS2 variants.
newscientist.com/article/226801…
On this topic, one major challenge is getting these new data (raw or assembled genomes) onto public databases ASAP.

I think there's some competition happening among the top databases. This has to stop for the duration of the pandemic. Priority is getting data public ASAP.
It can't be a situation where scientists and developers of vaccines, therapeutics, and diagnostics are learning about new variants from @TheScientistLLC @CNN etc.

Scientists need to have access to these data ASAP so we can optimize all the tools we have to fight this pandemic.
Read 6 tweets
17 Feb
Really good piece in ⁦@NBCNews⁩ by ⁦@KenDilanianNBC⁩ et al.

Questions about how large the covid outbreak was in Wuhan, how early it could’ve started, maybe even Sep 2019 if there were already dozens of unconnected cases in October.. nbcnews.com/health/health-…
Extremely challenging to answer these questions without access to thousands of banked patient samples from Wuhan from fall 2019, and the actual non-aggregated patient records from that time. Not just the 90+ shortlist but thousands of people with pneumonia in Wuhan fall 2019.
Office of Director of National Intelligence: agency "will continue to rigorously examine emerging information.. to determine whether the outbreak began through contact with infected animals or if it was the result of an accident at a laboratory in Wuhan" nbcnews.com/health/health-…
Read 6 tweets
16 Feb
On to my more contentious 🧵 of the night.

“It’s very funny that everyone is worrying about preprints given that, collectively, journals are not doing a great job of keeping misinformation out,” Sever (co-founder of medRxiv and bioRxiv) said.
washingtonpost.com/technology/202…
There's been a lot of criticism of preprints since COVID-19 appeared. I've done my fair share too, breaking down preprints (and mostly peer-reviewed articles).

But I think the misinformation tragedy lies in peer-reviewed journals, NOT preprints.
"In the academic world, the Center for Health Security at Johns Hopkins issued a point-by-point response one week after Yan’s paper appeared on Zenodo"

Why didn't John Hopkins do a point-by-points response to RaTG13 or the #pangolinpapers?
Read 12 tweets
15 Feb
Dear @WHO since you had a good conversation with Wuhan scientists, did you ask how many bats & coronaviruses they sampled in each province in China & when, & how many wildlife pathogen sequences they obtained from each province?

This is a question other scientists have asked me.
Without these numbers, it's hard to grasp the extent of risk associated with this research.

And I think even @EcoHealthNYC wouldn't know these numbers for each province in China. So I'm surprised that other scientists think I would know😆 My postdoc powers are very limited!
According to @MarionKoopmans the WIV told you they only isolated 3 SARS viruses from their decade+ of very expensive research. But what's the true value of their work? How many animals did they actually sample, and where and when? How many pathogen sequences were discovered?
Read 14 tweets
15 Feb
We heard from the @washingtonpost editorial board on the need to investigate #laborigins of covid-19.
washingtonpost.com/opinions/globa…

@WSJ editorial board is now also saying the lab hypothesis is important to investigate!

wsj.com/articles/who-a…
Live @WHO presser courtesy of @guardiannews:


Mike Ryan said WHO #originsofcovid mission didn't and doesn't have powers or mandate to investigate. What they participated in, inside China, was a "collaborative process of discovery."
Oh good, someone asked about the 13 early covid-19 virus genomes from Wuhan!

A few identical sequences were from the same individuals. Some sequences with no links to the market were slightly different.

Clarified! Not different strains.

Read 4 tweets
14 Feb
Interview of @Peterfoodsafety @WHO #originsofcovid investigation. On lab origins, “this would not be something that this team, or I believe even WHO alone, would be able to move forward on. That would have to be, I believe, a United Nations-wide approach...”
Well, we just heard it (or read it), and I agree with this assessment- if the international community wants an investigation of lab origins, this team and even WHO cannot be the ones investigating. We need a separate, credible, independent investigation into #laborigins of covid.
What are we waiting for?
Lab leak is a plausible hypothesis that should be investigated regardless of how likely or unlikely.
Read 4 tweets