Why “serious” scientists do not buy lab leak

“Serious” scientists doubt a lab origin because it is not permissible to consider intentional release.

Raccoon dog blues

If the zoonati — the biologists and other credential-havers who have defended the theory that SARS-CoV-2 autonomously crossed over into humans from nature, without any genetic manipulation — are “the enemy” of the truth, my impression is that they are a misunderstood one.

It’s often taken as a given that their work is disingenuous in toto. I think it’s important to understand that their position — if not some of the arguments supplied to defend it — is reasonable, if one’s only alternative to zoonotic origin is “gain of function” followed by accidental leak from the lab at Wuhan (i.e. WIV, the Wuhan Institute of Virology).

I’ve made this case before, but The Atlantic’s “raccoon dog” fiasco serves as a prompt to review the problem.

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The Atlantic.

A review of events:

1. In December, 2019, humans got sick who had been to Huanan Seafood Market in Wuhan, China. The market was closed on January 1, 2020; the Chinese CDC initiated swabbing of the market and identified animals on the same day and continued for three months. Researchers related to the investigation reported the following:

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   1. 64 of 848 (7.7%) environmental PCR swabs from within the market were positive for SARS-CoV-2.

   2. 0 of 457 animal samples (representing 188 critters, some stray residents of Huanan) were positive.

   3. 3 samples (a glove, a wall surface, and the ground), all taken on January 1, were successfully sequenced. Sequences related to these samples were not uploaded for open review.

   4. Overall, their results “suggested that SARS-CoV-2 might have been circulating in the market, especially the western zone, for a period of time in December 2019, leading to an extensive distribution of the virus within the market”

2. Members of the Zoonati have been actively monitoring the GISAID network for uploaded sequences of SARS-CoV-2. They caught a surprise upload of the Huanan sequences from Gao, et al., and downloaded them before the sequences were later removed.

3. (At least one of) these sequences contain(s) genes for both SARS-CoV-2 and for raccoon dog; being derived from a single swab, this means a swab rubbed up virus and critter genes in the same swipe. Therefore, the sequences are evidence, however conclusive, of SARS-CoV-2 infected raccoon dogs existing the same place as there were infected humans.

4. Katherine Wu, who is permanently glued to The Atlantic’s Pandemic Narrative Construction Desk, produced a scoop report of this development while (apparently) somehow not realizing that this would not establish whether raccoon dogs were the source of the virus, or merely caught it from humans (who caught it from somewhere else, or were infected in Huanan from other humans who caught it from somewhere else).

5. This obvious possibility was promptly pointed out by The New York Times.

6. I decided to use this prompt as an excuse to nuance-monger.

Barring new revelations, Wu’s article will stand as a cringe-inducing act of reputational self-harm. Her words:

But the new analysis [that maybe raccoon dogs got sick the same place humans did!] may offer some of the clearest and most compelling evidence that the world will ever get in support of an animal origin for the virus that, in just over three years, has killed nearly 7 million people worldwide.

A raccoon dog might have been infected on January 1! After weeks of nearby humans being infected! We did it, we cracked the case!

Wu’s saving grace may come in the form of the viral portion of the sequences — these may shore up the evidence for the raccoon dogs as a “source.” Gao, et al. reported finding two sequences matching “Wuhan-Hu-1,” and one matching the sister lineage “19b” of which 19a and all subsequent versions of the virus are probably a descendent. Their 19b sequence contained two additional deviations from Wuhan-Hu-1 besides the canonical “SNPs” (different-letter-havings) at positions 8782 and 28144. Is this (“A20”) the sequence slathered in delicious raccoon dog genes?

Gao, et al. Fig. 2 F13 and F54 represent the “newer” version of the virus which was sequenced first, and went on to found later variants (B.1 and progeny). A20 represents an “older” version which was sequenced later, as there were still ongoing human transmission chains with this version, especially in China, in early 2020.

If these two disagreements with Wuhan-Hu-1 and 19b bring the glove sequence closer to related wild viruses, it will lend to an argument that the genome predates known, contemporary human sequences. Even if so (I should check whether Worobey and co. previously commented on these SNPs):

It would remain that the glove in question could only have come into contact with raccoon dogs if a human were using it to touch raccoon dogs.

(“If the glove does not fit, you must acquit” — lawyer for raccoon dogs.)

The virus on the glove thus could still have been derived from a human (Gao, et al. reports that human DNA was reduced before sequencing to enhance the quality of the signal for RNA; I am not sure if this would remove mammalian DNA in the same proportion or not). Still, let’s say for now that the zoonati agents processing these furtively snatched sequences may have something else up their sleeve.

Without intentional US release, the case for lab origin is flawed.

Now we turn to my nuance-mongering. I have voiced my skepticism of the “lab leak theory,” emphasis on leak, on multiple occasions. I regard the stated aims and (putative) goings-on of Ecohealth Alliance’s relationship with the Wuhan Institute of Virology as either irrelevant, or a rather insultingly obvious op to frame WIV for an intentional release of the virus in Wuhan (by American government actors — whether as an attack on China, per Unz’s theory, or with the goal of initiating a so-called pandemic).

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And, it has become clear that the original claims that the virus leaked from WIV were seeded by American intelligence.

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Those who authentically and independently support the lab leak theory contend that “gain of function” research, of the type allegedly described in Ecohealth’s DEFUSE proposal and undertaken at WIV and elsewhere all the time, is America’s bioweapon program. To circumvent international agreements and taboos, the same government that can openly commit economic warfare on Europe with the destruction of a pipeline resorts to relabeling bioweapon development as “gain of function,” and thus we should all fret and bicker about why this type of research is allowed to continue.

The zoonati are operating in this same framework: Either the virus jumped from an animal, or it was a result of “gain of function” (which they would not label as biowarfare, but which is exactly what lab leak proponents insist is biowarfare, even if open to a blend of GOF and overt bioweapon development). The problem the zoonati have with the lab leak theory is thus that they know “gain of function” probably wouldn’t result in a virus like SARS-CoV-2; and even if so, it likely wouldn’t have happened at Wuhan.

As an outsider, I find their claims against lab leak more credible than the case for the same, regardless of what must surely be substantial conflict of interest on the zoonati’s part (they are the same actors conducting “gain of function” research). In short, both a zoonotic origin and a Wuhan lab leak strike me as heavily flawed theories of the origin of the virus; the framing of the controversy as only including these two alternatives thus ensures that both sides must miss the truth.

Some of these arguments against lab “leak” are more convincing than others. Recently, 163 sequences from WIV run and submitted to preprint review in 2018 were automatically published after a four year embargo.

In line with all results from the lab after 2019, no “smoking gun” sequences were included — nothing in the upload was closer to SARS-CoV-2 than “RaTG13,” and RaTG13, if it is even a real sequence, was not derived from a virus the lab was “growing” in culture or working on to any extent. It was a field PCR swab run through a sequencer to produce some values in a computer.

Zoonati-in-chief Edward C Holmes, however globally existential his conflicts of interest, concludes:

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This paper confirms what Zhengli Shi has said on RaTG13. No whole genome sequence was available for that virus and the WIV was clearly focused on SARS-CoV. These are the viruses they’ve isolated and cultured. There are no more viruses from the Mojiang mine.

The question that follows is why the WIV would then do GoF work on a divergent bat virus of no evolutionary nor biological importance and for which there was no complete genome sequence?

I had forgotten about this paper until the sequences were released on GenBank. I had forgotten because it was never published and all my emails were with Jie Cui (not Zhengli Shi) – a former postdoc I was helping and who normally worked on endogenous viruses/influenza.

This unpublished paper provides a snapshot of what bat CoV sequencing was going on at the WIV up to end of 2018. It was not easy to get whole virus genomes. A lab origin of COVID-19 would be proven if the progenitor of SARS-CoV-2 was in these data. It’s not.

An obvious conditional is that the Lab “leak” theory either strikes those most closely associated with the claims as improbably because it is, or because they have something to hide. How should outsiders determine which is the case?

Lab “leak,” whatever its corroborating evidence, struggles to explain certain facts, which include but are not limited to:

• If DEFUSE is an accurate and open “manifesto” of the work WIV intended to and did undertake in the years leading to 2019, including inserting human-appropriate cleavage sites into bat viruses of interest and evaluating effects in cell culture (page 11), why didn’t WIV publish details of any such experiments on the viruses they reported being interested in? In other words, not only would WIV have to have been conducting this work in secret on an unreported isolate of the precursor to SARS-CoV-2, but they would have to had either not taken such a step with their published viruses of interest, or have done so without reporting it. DEFUSE only has weight as evidence of guilt if what WIV did actually matches what DEFUSE says. It is more plausible that WIV’s work was in fact far more remedial and limited than what DEFUSE proposed, in line with what was published by the lab before 2020.

• Why is SARS-CoV-2 more closely related to bat viruses from Laos than the area frequented in WIV’s outings?

• Why did the virus emerge at the same time as the Military Games were held in China,

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  with reports of soldiers from many countries falling ill at the time?
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  Since the virus wasn’t noticed in the general population in Wuhan until December, how could soldiers at the Military Games have caught it “from Wuhan,” rather than bringing it to Wuhan? If east asians are more resistant to infection with the pre-Omicron strains of the virus, it is not impossible that an explosion of cases could occur in a group of visitors, but this would also require transmission from the same resistant populace. It is not plausible.

• Why did America (later) claim to know the virus was spreading in Wuhan in November, 2019, but not make the same claim for areas to which it had already additionally appeared by then (e.g. Italy, and probably California)?

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  This claim, if accurate, is suggestive of the US government being the agent of release, not WIV.

• Why did researchers from India report the HIV “inserts” in SARS-CoV-2 so quickly?

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  Note that no such immediate revelations have appeared for subsequent variants of SARS-CoV-2, such as the Omicron siblings, despite these variants presenting equally interesting genetic quirks. This is because normal "science" doesn't work this fast. Pradhan, et al. is more consistent with intelligence operation masquerading as authentic research (i.e., to drum up fear and conspiracy theories regarding the virus).

If intentional release is a simpler and less flawed account for these facts than a leak from WIV, why don’t the zoonati latch onto this as their counter-theory to lab leak, rather than an elaborate tale of raccoon dog misadventure (which is not satisfying regarding the same facts, but in fact may be more plausible than lab leak)?

Because “serious” scientists aren’t allowed to entertain the idea of deliberate release.

However flawed the zoonati’s case, therefore, it should be understood as a product of the taboos surrounding the topic. If only WIV is suspect for a lab origin, to the exclusion of import from elsewhere in order to frame WIV, then lab origin is not convincing.

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1. Wu, Katherine. “The Strongest Evidence Yet That an Animal Started the Pandemic.” (2023, March 17.) The Atlantic.

2. Gao, G. et al. “Surveillance of SARS-CoV-2 in the environment and animal samples of the Huanan Seafood Market.” researchsquare.com

3. See “I Could Have DARPED All Night.”

4. See “Lab Leak Op Confirmed.”

5. @edwardcholmes (twitter.com)

6. An October, 2019 starting point for human spread is consistent with the evidence, including pre-existing antibody levels (although Italy and California, two places with frequent travel from China, show evidence of the virus in late 2019, England does not, as reviewed here); and analysis of the evolution of 19a from 19b (reviewed here).

7. Reviewed by @alexandrosm (twitter.com)

8. See “Lab Leak Op Confirmed.”

9. Pradhan, P. et al. “Uncanny similarity of unique inserts in the 2019-nCoV spike protein to HIV-1 gp120 and Gag.” biorxiv.org