Kristian G. Andersen: Notice also where there were specifically is no clustering or early links - the lab. We would have expected that, did it start there - but that's not what we observe. Further, early epi data from market and non-market cases tell us that the market wasn't just an "amplifying" event.

When dealing with pseudoscience, the devil is in the detail - in this case, narrowing down a specific "Lab Leak" hypothesis. In Dr. Chan's @nytimes.com OpEd there is, however, a very specific hypothesis for COVID-19 origin. It's a prime example of conspiracism vs empiricism, so let's dive in. 🧵

On the day of Dr. Fauci's testimony, @nytimes.com decides to run a deeply unethical OpEd with snazzy graphics and snappy headlines about the Lab Leak. The article itself contains multiple falsehoods and deep mischaracterizations. Let's take every point in turn 👇🧵 www.nytimes.com/interactive/...

Opinion | Why the Pandemic Probably Started in a Lab, in 5 Key Pointswww.nytimes.com The world must not continue to bear the intolerable risks of research with the potential to cause pandemics.

If you read through the whole Opinion piece, Dr. Chan makes several specific claims, all of which would simultaneously have to be true for a Lab Leak to be a viable hypothesis. I will go through these in details below, but let's first list them:

1️⃣ The Wuhan Institute of Virology is the origin of the pandemic. 2️⃣ SARS-CoV-2 was at the WIV prior to the pandemic (it can't leak from a lab if it's not in the lab). 3️⃣ Dr. Zhengli Shi is the accused and is lying about it. 4️⃣ The virus was engineered. 5️⃣ WIV workers got infected/sick.

6️⃣ The virus escaped the lab, but early cases and hospitalizations were linked to a wet market. 7️⃣ The WIV covered up an early outbreak and has been covering it up ever since. All of these form a hypothesis Dr. Chan is putting forward in her piece. So let's take a look at the components in turn.

Below, I will use the structure of her article so it is easier to follow. I will take each point and then compare that to what we actually know to be facts or specific conclusions informed by available evidence.

1️⃣ The Wuhan Institute of Virology is the origin of the pandemic. 2️⃣ SARS-CoV-2 was at the WIV prior to the pandemic. 3️⃣ Dr. Zhengli Shi is the accused.

So this is rather specific. The WIV is the origin of the pandemic and hence the virus must have been in their holdings prior to the pandemic. A specific scientist - Dr. Shi is also being accused of being the person responsible. The problem is, we have no evidence of any of this being true.

For example, here is what US Intelligence Community concluded in their most recent report: "no indication that the WIV’s pre-pandemic research holdings included SARS- CoV-2 or a close progenitor" Report: www.dni.gov/files/ODNI/d...

They also concluded: "Information available to the IC indicates that the WIV first possessed SARS-CoV-2 in late December 2019, when WIV researchers isolated and identified the virus from samples from patients diagnosed with pneumonia of unknown causes.

All of this is in direct contrast to Dr. Chan's statements. It *is*, however, highly consistent with the fact that we can find absolutely no trace of SARS-CoV-2 having been at the WIV prior to the pandemic. And it's not from lack of trying.

It's just that it just isn't there and it doesn't matter where we look. Importantly, however, *any* Lab Leak hypothesis requires the presence of the virus in a lab prior to the pandemic. Yet, such evidence does not exist.

4️⃣ The virus was engineered. A few things here. (1) This would have required that the WIV (rather miraculously) found a pre-pandemic virus before it found us, (2) they engineered it (inserted an FCS to follow later logic), and (3) that created a pandemic virus (which took off in a market...).

There's more specifics to this claim - it has to do with "DEFUSE", which you can get here: drasticresearch.org/2021/09/21/t.... The problem is, pretty much everyone - and certainly anybody who has done such engineering work previously - agree the virus wasn't engineered. Really? Well yes...

As I mentioned in my prior thread, the DEFUSE proposal doesn't actually present a "blueprint" for the features observed in SARS-CoV-2. Here's what it actually says in the relevant section (note, the FCS is at the S1-S2 junction in SARS-CoV-2).

Dr. Baric gave more specifics on this in his testimony and also stated that the virus wasn't engineered. Full transcript here: oversight.house.gov/wp-content/u... Example 1 from Dr. Baric:

Example 2 from Dr. Baric:

And in case you might have heard about "oh, but restriction sites", there are two fatal flaws that makes any further discussion of that 'study' moot: (1) the same restriction sites can be found in related viruses, and (2) many other viruses would also be classified as "engineered". Dr. Baric:

We concluded exactly the same in our 2020 "Proximal Origin" paper that this isn't an engineered virus. pubmed.ncbi.nlm.nih.gov/32284615/

The proximal origin of SARS-CoV-2 - PubMedpubmed.ncbi.nlm.nih.gov The proximal origin of SARS-CoV-2

And, finally, to that point, the intelligence community also agrees that SARS-CoV-2 wasn't engineered.

Getting back to point #3, but now about the "lying" and "cover up" part. 3️⃣ Dr. Zhengli Shi is the accused and is lying about it. In this particular case, by deleting a database. The timing isn't mentioned here, but it's important because people describe this as being September, 2019.

If the WIV deleted a database in September, 2019 to cover up infections at the lab, then the pandemic must have started no later than September. The problem is - it didn't. You can look at epi, serological, or genomic data and it doesn't matter - the pandemic very likely started ~mid November.

Here's a recent article estimating the timing of the pandemic based on epidemiological data: pubmed.ncbi.nlm.nih.gov/38457460/

Using early detection data to estimate the date of emergence of an epidemic outbreak - PubMedpubmed.ncbi.nlm.nih.gov While the first infection of an emerging disease is often unknown, information on early cases can be used to date it. In the context of the COVID-19 pandemic, previous studies have estimated dates of ...

Molecular dating requires care and, importantly, paying close attention to sequencing and informatics artifacts. We did that here and also get ~mid November timing: pubmed.ncbi.nlm.nih.gov/35881005/

The molecular epidemiology of multiple zoonotic origins of SARS-CoV-2 - PubMedpubmed.ncbi.nlm.nih.gov Understanding the circumstances that lead to pandemics is important for their prevention. We analyzed the genomic diversity of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) early in the...

Here's a comprehensive study using serology on banked samples obtained prior to the pandemic - same conclusion. academic.oup.com/proteincell/...

Serosurvey for SARS-CoV-2 among blood donors in Wuhan, China from September to December 2019academic.oup.com Abstract. The emerging of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) caused COVID-19 pandemic. The first case of COVID-19 was reported at

Let's lump these next parts together: 6️⃣ The virus escaped the lab, but early cases and hospitalizations were linked to a wet market. 7️⃣ The WIV covered up an early outbreak and has been covering it up ever since. First, with a claim about the biosafety:

I already addressed the issues about the biosafety in my previous thread, but let's take the part where it's insinuated that some sort of accident must have happened. As above, we don't have any evidence for that - here, again, the ODNI report:

Okay, but maybe it wasn't an "accident", per se, it's just that workers got infected and got sick. Note, the timing here is important because this is suggested to have happened in November, 2019. Which, of course, doesn't match the suggestion that the database was deleted in September, 2019.

As I already stated, ODNI disagrees on this "intelligence", but there are other issues: 1️⃣ Again, it's inconsistent with the prior claim of September, 2019. I have already pointed out that it wasn't actually September, 2019, but all the way into 2020. So let's discount this.

2️⃣ But there's a bigger problem with that claim - if three young people were to have been sick (and potentially hospitalized) with COVID-19 in November, 2019 at a single facility in Wuhan, then the pandemic would have to have been rampant at that point and certainly at the WIV.

But it wasn't. We know that. Further: 3️⃣ We would expect some sort of link between the early cases and the WIV, outside just the three that, allegedly, got sick. But we don't have that - the evidence, as we will get to, points elsewhere.

Before I get to the last few claims, I want to get back to this part again: 3️⃣ Dr. Zhengli Shi is the accused and is lying about it. First, we're talking about a named scientist and she's being accused of being responsible for the deaths of millions. She's a person.

She has, repeatedly, denied all accusations. She says she tested all her staff for COVID-19 and they were all negative. She says they did not have SARS-CoV-2 in the lab prior to the pandemic and checked her samples, records, etc., to make sure that to indeed be the case. Yet, she remains accused.

So from all of this, anybody who claims she was responsible for having created SARS-CoV-2 is also - based on absolutely no evidence - accusing her of lying. We also have no evidence for that. In fact, she has given several interviews and many of her statements could later be tested and verified.

This is why there is no "innocent" version of the Lab Leak, because it always comes back to accusing specific individuals of being responsible, for lying, and for being part of a cover-up. With no evidence. No matter how a Lab Leak writer might try to hide that inconvenient truth in their writing.

If you believe that SARS-CoV-2 came out of a lab, I suggest you keep that in mind and then read the interviews with Dr. Shi. www.science.org/doi/10.1126/... www.science.org/pb-assets/PD... www.technologyreview.com/2022/02/09/1... www.nytimes.com/2021/06/14/w...

Wuhan coronavirus hunter Shi Zhengli speaks outwww.science.org China's "Bat Woman" denies responsibility for the pandemic, demands apology from Trump.

Alright, so now to the final point, which I did not mention up front: 8️⃣ The data currently available to us is crap... Now, this is where we are seeing a clear split between conspiracism and empiricism. Because not only do we have well-informed priors, we also have a rich extant evidence base.

Dr. Chan likes to highlight the fact that, shocker, there's actually still data missing. But on the "zoonosis" side, at least there *is* actually data and you could simply flip her argument to say that literally everything we would expect to find for a Lab Leak is missing.

More importantly, the "key" evidence that is missing is simply nothing more than an infected intermediate host - which we only have in extremely rare cases and, as I made clear in my original thread, require that we actually go looking for it. So let's take a look at the actual evidence.

But before doing this, I want to make this clear. We're not talking about what's "possible". Anything is "possible", including a lab leak, and in the absence of specific evidence, talking about what is "possible" is a great way to generate hypotheses.

But we're long past that. We're on to what's "probable". To get from "possible" > "probable" we first establish "priors". Those priors should, ideally, be well-informed, which requires, at a minimum, experience and expertise. Ideally, we also have precedence from prior events.

Let's establish our priors. In my original thread I made the points that given (1) diversity of SARSr-CoVs, (2) how widespread they are, (3) our many interactions with them, and (4) rampant trade in wild-life, bringing them into dense human networks, zoonosis >>> lab without any other data.

Now, let's start informing those priors a little more specifically - in this case, precedent. SARS-CoV-1 vs SARS-CoV-2 look remarkably similar - from the virus itself, to the association with wet markets and the November timing. Not to mention, SARS-CoV-1 positive animals were only found in Hubei.

Let's move on to specific hypotheses. As already shown, the one put forward by Dr. Chan does not stand up to any scrutiny whatsoever - even in the absence of looking at any of the extant data (in which case, like other Lab Leak ideas, it collapses). What about zoonosis?

Under a "zoonosis" hypothesis, there are several things we would expect to be true: 1️⃣ Early cases should be associated with high risk exposures to animals. 2️⃣ Specifically, given SARS, a likely emergence would be associated with a wet market, restaurant, or other network in an urban setting.

That is exactly what we see. The outbreak itself was detected at the levels of hospitals noticing people coming in with unknown pneumonias, with a large proportion having direct connections back to the Huanan Seafood Market. pubmed.ncbi.nlm.nih.gov/34793199/

Dissecting the early COVID-19 cases in Wuhan - PubMedpubmed.ncbi.nlm.nih.gov Elucidating the origin of the pandemic requires understanding of the Wuhan outbreak.

If the market was indeed the place the pandemic started, we would expect cases to cluster around the market - in addition to what was observed at the levels of hospitals. As we, retrospectively, look at early cases, that is exactly what we see. pubmed.ncbi.nlm.nih.gov/35881010/

No, this clustering is not down to some imaginary "bias" - that's clear from just looking at the distribution of the data itself. You can also read our original paper where we address potential bias in detail, or this recent preprint: arxiv.org/html/2405.08...

No evidence of systematic proximity ascertainment bias in early COVID-19 cases in Wuhan Reply to Weissman (2024)arxiv.org

Notice also where there were specifically is no clustering or early links - the lab. We would have expected that, did it start there - but that's not what we observe. Further, early epi data from market and non-market cases tell us that the market wasn't just an "amplifying" event.

If we look at the market itself, it's a very unlikely place for an outbreak to have started, if it wasn't for the high risk exposures to potentially infected animals. There are *many* other places *much* more likely for an outbreak to take off in a big city. Yet, it was the market.

So early hospitalizations and cases point to the market. Since, once the outbreak was detected, authorities clamped down to, one might also expect to see a signal in early excess deaths in the area where the market is located. That is exactly what we observe. pubmed.ncbi.nlm.nih.gov/34480864/

In addition to early hospitalizations, cases, and excess pneumonia deaths, serological signatures also point to the market, with later studies showing that the area where the market is located had the highest levels. pubmed.ncbi.nlm.nih.gov/33585828/

Most SARS-CoV-2 transmission chains die out and pre-outbreak, risk factors are related to getting just the right context (the right virus, the right infected animals, the right conditions, the right human density, etc), but once those exist, we're off to the races.

Given those conditions under a zoonosis hypothesis, you would expect multiple spillovers to occur, with most of those likely going extinct. However, we see clear evidence of multiple spillovers having occurred - at a minimum two distinct ones. pubmed.ncbi.nlm.nih.gov/35881005/

Importantly, those early "lineages" were both associated with the Huanan Seafood Market - which is exactly what we would expect had the pandemic started there.

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