Explosive Huanan findings, revealed: Raccoon dog DNA at same place as... raccoon dogs.
Even the unimpressive preview by Wu was an overstatement.
Summary: Nothing to see here
The “zoonati” (see previous post for description) have uploaded their report on the sequences from the Huanan seafood market uploaded to the global virus gene sharing network, GISAID.1 The incredible findings:
PCR-positive samples from areas where animals were already known to be sold, including raccoon dogs, had animal genes.
That, apparently, is it. The claims made by The Atlantic’s Katherine Wu of animal and viral genes being on the “same swab” apparently do not refer to the three samples which were successfully sequenced by Gao, et al.
Instead, there just happen to be various types of mammalian DNA on various PCR positive samples; as there would surely be on many PCR negative samples taken at the same site.
As such, nothing seems remarkable about these breathlessly reported discoveries beyond the antagonism on display between the zoonati, GISAID, and the world at large which has turned its back on natural origin (more below).
Summary of Crits-Cristoph, A. et al.:
The Huanan seafood market was closed on January 1, 2020, after people who had been there got sick. The Chinese CDC went in and took a bunch of samples of surfaces. Some would prove to be PCR positive for SARS-CoV-2, mostly in the western corner where many animal stalls were located, as later reported in pre-print by Gao, et al.; but sequences and associated data were never made publicly available.2
Another Chinese research team happened to have been surveying animal sales in the months prior to those illnesses.3 They eventually reported nearly 40 raccoon dogs sold a month during their 2019 survey, so there was never any doubt that raccoon dogs (and other animals susceptible to the virus, marked “s” below) were at the scene of the “outbreak” at Huanan.
The zoonati found some raccoon dog genes in some files uploaded in association with the Gao, et al. pre-print! Proving the animals we already knew were at Huanan… were at Huanan.
By disclosing their findings on Gao, et al.’s proprietary files, the zoonati have “gone rogue” (my words) against the GISAID network, simultaneously accusing the same entity of violating its founding mission of facilitating the rapid, open assessment of viral genetic data. Spicy!
We may now discuss interesting particulars.
Plot twist: Are the zoonati the dangerous ones now?
In apparent retaliation for point 4 above, GISAID has cast some of the authors’ login credentials out to the wilderness, declaring them “excommunicado” (my words) from the global virus gene sharing network.
Wu now reports:
This morning, hours after the researchers released their report online, many of them found that they could no longer log in to GISAID—they received an error message when they input their username and password. “They may indeed be accusing us of having violated their terms,” Moshiri told me, though he can’t be sure.4 The ban was instated with absolutely no warning.5
This is actually happening — the zoonati are at this moment actually living out the opening scenes to John Wick 3.
Regardless of lack of a warning, their excommunication is presaged in the introductory remarks of their report, which are laden with tension — the authors, once the same assassins who had leveraged Gao, et al.’s work to dispatch the “lab leak theory” on behalf of the mainstream narrative, knew they were now inviting the retribution of their viral genome guild. After detailing the day-by-day interactions with Gao, et al., GISAID, and the WHO that had led from March 9 to this moment:
We acknowledge that these circumstances are unusual. We are proponents of open data sharing, and ensuring that data from our analyses are broadly accessible in public repositories is our standard practice. […]
But despite this transparently exciting situation, it remains that nothing is really noble about the zoonati’s quest. As always, their new report and associated tweets operate in a fantasy-land where zero evidence of the virus’s October, 2019 emergence, and early international dissemination, and mutation to B.1 abroad are acknowledged.7 Moreover, the "findings" which they have sacrificed their logins to report are of such low quality and weight that no insights are delivered.
Results vs. Hype
Revisiting Wu’s claims from last week, while she is careful to qualify the new findings as falling short of proving animals were infected, she nonetheless portrays them as robust within those limitations (emphasis added):
Within about half a day of downloading the data from GISAID, the trio and their collaborators discovered that several market samples that tested positive for SARS-CoV-2 were also coming back chock-full of animal genetic material—much of which was a match for the common raccoon dog […]
Finding the genetic material of virus and mammal so closely co-mingled—enough to be extracted out of a single swab—isn’t perfect proof8
A visit to the supplemental materials of the newly posted report displays findings for 225 uploaded GISAID files, only 6 of which contain sequences matching raccoon dog mitochondrial genes. None are from the three samples that went on to produce successful sequences of SARS-CoV-2 and/or cell cultures.
This does not mean that no other samples had raccoon dog genes, per se — there might have been some hits missed due to selection of which genes to use for alignment. Nonetheless, it is unimpressive in the extreme.
In Conclusion - no meaning to the “co-mingling”:
Nothing seems remarkable about the fact that environmental samples in a market selling animals would find animal genes. No conclusions can be made about the supposed “co-mingling” of these genes without knowing the mammal-positivity rate for SARS-CoV-2 negative samples (a point halfway acknowledged in the zoonati report); and only very weak inferences could even be made with that information.
No mammalian “finger-prints” were found on the most important three samples, those which produced sequences for the virus.
None of this is necessarily the zoonati’s fault. It is more the case that Nature doesn’t often “leave receipts.” In the simpler world of the SARS-1 era, for example, it was enough to merely find a related virus in a palm-civet months after the appearance of the virus, which actually doesn’t prove anything about how SARS-1 emerged. The zoonati are being held to a quasi-impossible standard, however disgracefully and disengenuously they have tried to meet it.
Just “Shedding New Dark”?
Beyond being inconclusive, the results reported in Crits-Cristoph, et al.’s supplemental materials reflect some peculiar anomalies, suggesting possible errors in provenance which make associations between mammalian genes and given sample IDs hazardous.
For example, five (of the six) samples positive for raccoon dog are five (of the six) samples with inconsistent, ambiguous reporting for PCR values in Gao, et al.’s table 1:
Given the contradiction between the stated criteria for Table 1 and the reported PCR results, it would seem that at the time of preparing their preprint, Gao, et al. no longer knew why these samples had been included in their sequencing attempt to begin with.
The three samples which successfully produced sequences for SARS-CoV-2, meanwhile, are all “clean” of non-human mammalian genes:
This is consistent with roughly half of the files uploaded by the Chinese researchers and dissected in Crits-Cristoph, et al., so it isn’t overtly suggestive of anything having been “scrubbed” before upload. However, as long as Gao, et al. aren’t actually going to let anyone else look over their shoulder, it doesn’t seem like there is any value to reading into the available data to infer anything beyond the obvious (there were some sick humans at Huanan in December, and so of course there could have been some sick animals there, which wouldn’t prove anything about where the virus came from).
If you derived value from this post, please drop a few coins in your fact-barista’s tip jar.
Gao, G. et al. “Surveillance of SARS-CoV-2 in the environment and animal samples of the Huanan Seafood Market.” researchsquare.com
Xiao, X. et al. “Animal sales from Wuhan wet markets immediately prior to the COVID-19 pandemic.” Sci Rep. 2021 Jun 7;11(1):11898.
“OTOH, maybe it was raccoon dogs what stole our accounts” — Moshiri
Wu, Katherine. “A Major Clue to COVID’s Origins Is Just Out of Reach.” (2023, March 21.) The Atlantic.
(Crits-Christoph, A. et al.)
Amendola, A. et al. “Molecular evidence for SARS-CoV-2 in samples collected from patients with morbilliform eruptions since late 2019 in Lombardy, northern Italy.” Environ Res. 2022 Aug 25;215(Pt 1):113979.
The mutation “D614G” on the spike protein appears in association with the development of B.1 (which includes co-fixed mutations at 3037 and 14408 of the sequence), which appears to occur in Italy in late 2019:
Wu, Katherine. “The Strongest Evidence Yet That an Animal Started the Pandemic.” (2023, March 17.) The Atlantic.