Defending the case against a WIV origin

Response to reader comments to my "only intentional release makes sense" argument. Plus: A new manual sequence alignment for the spike protein.

This post seeks to defend my “leave WIV alone” argument, and to debut a manual alignment of the sequences for the structural portion (including spike protein) of SARS-CoV-2, BANAL52, and “RaTG13.”

The SARS aligned

The authors who published the northwestern Laos bat viruses that seem to be the origin or “template” from which SARS-CoV-2 was created demonstrate, in their paper, that “BANAL-20-52” has high resemblance to that virus in the receptor binding domain, but maybe less of a clear advantage over RaTG-13 in other elements of the spike protein.¹ Since there are doubts whether the sequence the Wuhan Institute of Virology uploaded for RaTG-13 is authentic, it never occurred to me to try a comparison for myself.

Now that it turns out a RaTG-13 sequence was submitted by the lab back in 2018, it seems more appropriate to analyze it and assess whether it is or is not evidence tying the lab to SARS-CoV-2. This will be attempted in a subsequent post. For now, here is the file for those who want to dig in:

https://www.icloud.com/iclouddrive/0e5h8kSD_iLK_N0IPWL9XWsTw#sequence_map_sarscov2_aligns_share

Additionally, the “Resource Hub,” which contains my other adventures in “brute-force genomics,” has been updated with recent posts and given a table of contents to make it more user-friendly:

Follow-up to the Leave WIV Alone argument, pt. 1

Readers have provided some excellent push-back to my argument against the (non-intentional, Wuhan Institute of Virology-based-) lab “leak” theory in the comments to last week’s post (my argument is that a lab origin is only more plausible than natural origin when intentional release of a virus developed outside of Wuhan is considered possible).

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Why do I keep ruling out “rogue actor”?

Commenter “jman” asks:

So the options are zoonotic, leaked, spread, and there is no virus?

I might divide spread into intentional by agency, rogue or not, and intentional by individual, as in a kind of Malaysian flight 370. But I don't know how hard it would be to start a pandemic, maybe Daszak or Baric can chime in here.

I keep neglecting to mention rogue actor release because… I keep forgetting it! Although I find the standard “leak” scenario implausible, it is not true that “US government intentional release” is the only kind of “intentional release” possible. However, this would render puzzling all the evidence that suggests government (and super-governmental actor) “preparation,” of which there are more than zero.

Still, rogue, “hacker”-style development and release is plausible.

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Is the “HIV Inserts” pre-print suspicious?

Commenter “John G” writes:

I watched the comments section on their pre-print before it was pulled and it reminded me of how Dr. Henrik Svensmark was treated at a scientific conference when he presented his sun spot cycles tied to global temperatures paper. Vicious. And to the best of my reading, the HIV insertions proved real...although odd that not much seems to have come of that finding. As a result, I missed your clear red flag finding of "major epidemic..." in the very first line no less. So, I emailed and asked them (didn't mention you). You'll never know if you don't try :)

I replied by pointing out the curious reference to “major epidemic” in the same preprint, which, again, was uploaded on January 31, 2020.²

Incredibly, John G was able to get a reply from the corresponding author regarding the same question:

Wow! They replied. Here it is........."A simple search on the internet would reveal that by March 2020, WHO had already designated SARS Cov2 as a pandemic.

Before that there were newspaper reports of rapid spread of this disease.

On 30 January 2020, the World Health Organization (WHO) declared the current outbreak of the novel coronavirus 2019‐nCoV, which was first detected in the Chinese city of Wuhan on 31 December 2019, a “public health emergency of international concern”—an alarm it reserves for events that pose a risk to multiple countries and which requires a coordinated international response. (Please see this paper by - Wu D, Wu T, Liu Q, Yang Z. The SARS-CoV-2 outbreak: What we know. Int J Infect Dis. 2020 May;94:44-48. doi: 10.1016/j.ijid.2020.03.004. Epub 2020 Mar 12. PMID: 32171952; PMCID: PMC7102543).

By the time we reported, we had this WHO information just came in. Moreover, Cases of mild to severe illness, and death from the infection have been reported from Wuhan. The number of cases within and outside China were increasing steeply. By the time our report came the outbreak had spread rapidly to distant nations including France, Australia and USA among others.

I hope this satisfies your query.

Best wishes,

B. Kundu"

Fair enough — if the “major epidemic” verbiage was indeed a last-minute declaration. Of course, that would be an incredible coincidence — despite just naturally rushing to publish their findings as soon as possible, the WHO declared a public health emergency a few hours before. Nor would this coincidence be inconsistent with, well, some sort of “planned” release of the HIV revelations.

Still, I would like to set the Pradhan, et al. question aside. The sequence alignment, discussed in the next post, will show that these notorious “unlikely” resemblances to HIV do in fact seem to be random chance (except perhaps for the furin cleavage site insert) — three of them can be found in wild coronaviruses, and so they are unremarkable except when inappropriately comparing SARS-CoV-2 to the much more distantly related SARS-1.

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What if UNC designed the spike and sent it to Wuhan — couldn’t that still result in an oopsie?

Commenter “Mass” writes,

You’re missing an important data point.

The lab work was meant to be done in North Carolina by Baric. According to J Sachs who spoke to a DEFUSE reviewer, the work was done before the proposal went in.

This would not change whether the rest of SARS-CoV-2, as it emerged, was among the Wuhan Institute of Virology’s viruses of interest, which they were known to have made DNA<>virus (a.k.a. “infectious clones”) backbones of for inserting things into. If UNC sent the SARS-CoV-2 spike attached to one of those viruses, we would see that the rest of SARS-CoV-2 carried those genes. If UNC had sent it attached to what did get released — i.e. the rest of the virus’s genome — WIV would presumably have emails in which they remarked and enquired on the appearance of this new “backbone.” Such “uh, Baric, where did all these genes come from?” emails would exonerate WIV and China; but we haven’t seen such emails.

Alternately, one can suppose that WIV was working on a (BANAL-based) progenitor without telling anybody; but at that point one is weighting circumstantial evidence and imagination over what has actually been published and discussed by WIV.

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Reminder: WIV and “GOF” are not necessary

Some of the other comments essentially recycled the consensus meta-narrative around lab “leak” at me — even though that is exactly the meta narrative I am attempting to refute. If I write posts with the premise, “I know everyone thinks X, but here is why Y,” comments to the tune of “Everyone thinks X!” are not going to raise any points I have not already heard.

Generally, the problem with the consensus narrative around WIV and Gain of Function is the smuggled presumption that some elaborate system of international coronavirus “pandemic prevention research” is necessary to create an unnatural virus that can infect humans. But it isn’t. WIV and GOF can be seen as “extra parts,” absent any indication that their work actually points to (the genetic signature of) SARS-CoV-2. Instead, it points away — they were mired down in other “backbones.”

One may liken WIV to any organization that “has been working on something” for a long time. If they haven’t made progress on the path they are on — the “WIV-1” construct, etc. — they aren’t tomorrow suddenly going to produce a complete product from a totally fresh start. Absent leadership and staff change, WIV was less likely to create SARS-CoV-2, which is based on BANAL type viruses that are not anywhere in their published material, than any lab somewhere else in the world starting fresh.

BANAL may seem like an obvious template in retrospect — but before 2019, this family of viruses had not (as I understand; correct me if I am in error) been identified. Even if these viruses were already interacting with humans to some extent — antibodies may have pre-existed to BANAL52 in Myanmar³ — there was no way to detect and realize this interaction absent culturing of the virus by someone. This is the case even for universally prevalent human viruses — again, the example being NL63, which was not discovered until 2004 but proved to be universally recognized in adults by antibodies.⁴

But if SARS-CoV-2 is a genetically modified outcrop of a BANAL-related progenitor, then by definition, some entity went and collected some BANAL viruses and cultured them, without publishing the results — and this entity is the creator of SARS-CoV-2.

(Alternately, both RaTG13 and BANAL52 are fakes, and the genetic data does not mean anything — however, such a claim is not in any way evidence implicating WIV.)

Thus, in the next post, we will look at the sequence alignment to further the case that BANAL, and not WIV’s “RaTG13,” must have been the source material, and re-evaluate the genetic argument against a natural origin (it is a bit weaker than it seems).

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1. Temmam, S. et al. “Bat coronaviruses related to SARS-CoV-2 and infectious for human cells.” Nature. 2022 Apr;604(7905):330-336.

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

3. Evans, TS. et al. “Exposure to diverse sarbecoviruses indicates frequent zoonotic spillover in human communities interacting with wildlife.” Int J Infect Dis. 2023 Mar 2;S1201-9712(23)00064-4.

The limit here is that only a “small fraction” of samples seem to have been collected before 2020; therefore, SARS-CoV-2 itself may be causing cross-seropositivity to BANAL52 in samples. It is nonetheless an interesting new study, given that it apparently stems from the final mission of the USAID’s PREDICT program.

4. Hofmann, H. et al. “Human coronavirus NL63 employs the severe acute respiratory syndrome coronavirus receptor for cellular entry.” Proc Natl Acad Sci USA. 2005 May 31;102(22):7988-93.