The raccoon dog theory
One very famous molecule!
“This is a really strong indication that animals at the market were infected. There’s really no other explanation that makes any sense.” - Angela Rasmussen, University of Saskatchewan virologist, March 16, 2023
“We never claimed to find infected animals.” - Angela Rasmussen, University of Saskatchewan virologist, April 28, 2023
“Nothing needs to be exposed since it's already barefaced.” - Toni Morrison
Is it just me, or are you too feeling beaten down by the bamboozle lately?1
You probably noticed the deluge of headlines back in March about a connection between the pandemic and raccoon dog genetic material found at the wet market in Wuhan where some scientists maintain the pandemic began.
Yet you probably haven’t heard that the theory largely hinges on one measly molecule.
The raccoon dog controversy is, of course, mostly about the science. But there’s another story here about human behavior — about DRAMA — one that I’m worried will be lost to pandemic history. A peek under the hood of the deceptively dry scientific reports reveals bitter rivalries, hypocrisy and hubris among our most prominent virologists.
China CDC
In March, crusading Western virologists sleuthed data demonstrating the presence of coronavirus-susceptible animals, namely raccoon dogs, in the wet market in Wuhan, fearlessly defying the censorious Chinese Community Party … or so they told reporters.
In fact, the data had been uploaded by Chinese scientists to the popular genomic database GISAID as they prepared to publish a study in Nature, among the most famous scientific journals in the world.
A preprint published in early 2022 provided a preview of the Chinese scientists’ paper:
In addition to testing 188 animals in the market for the virus (all negative), the Chinese Center for Disease Control and Prevention team had analyzed genomic data picked up in swabs taken from around the environment of the wet market and found 73 positive samples. They then mapped how the virus correlated to the various animal species detected in the samples.
They concluded that the data did not implicate any particular animal as the intermediate host of the virus and recommended further study.
Among the species found to most strongly correlate to the virus: homo sapiens.
Combined with other findings,2 the data pointed to “amplification” at the wet market. In other words, a superspreader event.
“The market might have acted as an amplifier due to the high number of visitors every day, causing many initially identified infection clusters in the early stage of the outbreak,” the paper stated.
However, while the Chinese scientists plotted positive samples against species detected in the market, the preprint did not denote the species.
The omission of this data miffed prominent Western virologists Michael Worobey and Edward Holmes, who argue that a wet market origin is THE ONLY (all caps) plausible source.3
They have often speculated about raccoon dogs in particular, including in their earlier scientific publications.
In a serendipitous visit to the same wet market years earlier, Holmes had snapped a photograph of a caged raccoon dog — apparently becoming the white whale to Holmes’ Ahab.
Political intrigue … or professional rivalry?
To be sure, there are still many unanswered questions about the year-long delay in the China CDC paper’s publishing in Nature and why the accompanying environmental data was unavailable for so long.
Politics could be at play.
Since at least April 2020, every Chinese publication about the virus’ origin requires approval from the country’s Ministry of Science and Technology.
Also worrying: Lead author William Liu of the China CDC was a member of the conflicted and censored WHO-sponsored COVID-19 origins investigation, calling into question his credibility.4
Like the WHO investigation, the China CDC paper lent credence to Beijing’s science-free propaganda that COVID-19 came into the seafood market through foreign cold chain products. (From Fort Detrick via Maryland crabs? Never been clear on this one.)5
But Chinese politics may not be wholly to blame in this instance.
In a 2022 news story, a peer reviewer on the China CDC paper anonymously told a reporter that they would hold up its publication until the environmental data was made available.
It’s not clear whether any of the Western virologists involved with the rapid reanalysis of the China CDC data were also peer reviewers on their paper. However, it is clear that Holmes and Worobey were also quoted in that same Science story.
(For what it’s worth, when I asked former China CDC scientist George Gao about it, he responded that he didn’t believe the quote was authentic because it is not permissible behavior in science to speak to the media about the peer review process.)
It’s also clear that the China CDC scientists had already been scooped and overshadowed by Worobey, Holmes and Andersen using their data once before, and they had good reason to be wary it could happen again.6
In any case, soon after the Chinese scientists’ environmental data appeared on GISAID, Western virologists scooped it. Crusaders indeed.
The media frenzy
Within a few hours of downloading the data, according to news reports, the Western virologists had begun tittering in the Zoo Crew group chat: “raccoon dog, raccoon dog, raccoon dog.”
Before any polished analysis had even been committed to writing, they were talking to the World Health Organization and The Atlantic about their favorite fuzzy intermediate host.
One positive sample in particular, Q61, was chock full of raccoon dog genetic material and contained little human genetic material.
“Think of it as finding the DNA of an investigation’s main suspect at the scene of the crime,” reported The Atlantic, which dubbed the data the strongest evidence yet in favor of a zoonotic origin.
“Other scenarios require contortions of logic,” the story read.
The analysis was led by none other than Worobey, Holmes, and virologist Kristian Andersen according to The Atlantic’s report.
One glaring problem: Holmes and Andersen are being scrutinized by Congress due to evidence they misled the public on this very topic on an enormous scale in early 2020, a red flag for the scientists paying close attention even before the data or analysis was made available.
In fact, the private notes of Holmes and Andersen from February 2020 betray deeper ambivalence about the wet market being the origin than they publicly let on. (“The connection to the market would be spurious – some doubt on that already.”)
The journalist behind The Atlantic’s report and the dozens of reporters who wrote copycat stories did not appear deterred by the data scooping, the pattern of deceit, or the lack of any tangible analysis to independently once-over the virologists’ claims.
The Western virologists also made another bold claim: They accused the Chinese scientists not only of sloppy analysis but of being tools of a “bloody scandal.”
They told a gripping tale of international intrigue: The Chinese scientists had quickly pulled their data from the database due to a coverup of the raccoon dog origin of COVID perpetrated by the CCP. (Some of them even assert that Beijing would be more humiliated by an origin in illegal wildlife than by an origin in a lab with military ties.)7
Yet the Western virologists neglected to mention to the world that they were at that very moment receiving emails alerting them to the Chinese scientists’ concerns not about politics, but about their data being stolen.
Holmes, Worobey, Andersen and others on the Western team ignored appeals from the database’s leadership about the Chinese scientists’ concerns about scooping. That is, until they found themselves locked out of the database.
The database’s leadership accused the Western virologists of an “unprecedented” breach of research ethics, and at the very least, bad manners. The database’s leadership took the equally unprecedented step of revoking their access to one of the largest genomic repositories in the world.8
When the database temporarily restored their access as an act of goodwill as they investigated the controversy, Florence Débarre, an evolutionary biologist involved with the analysis, took a screenshot and posted it to Twitter to demand an apology, falsely implying that she and her collaborators had already been cleared of any wrongdoing.
Yet in all of this hubbub, the Western virologists hadn’t actually directly rebutted the initial analysis conducted by the Chinese team — the one that correlated the abundance of SARS-CoV-2 detected in the environment to the abundance of animal genetic material.
They hadn’t meaningfully confronted what Gao said back in 2020: That the market was “just another victim.”
Yet the media fanfare ignited by these virologists implied a relationship between the virus and raccoon dogs.
“New covid origin data links raccoon dogs to the pandemic,” read one headline.
“New data links pandemic’s origins to raccoon dogs at Wuhan market,” read another.
But to what degree was raccoon dog genetic material actually linked to the source of the pandemic, SARS-CoV-2?
While they had analyzed the abundance of various animals in the samples, and they knew the samples had been classified as “positive” by the Chinese team, they did not report on how much SARS-CoV-2 had been detected in those samples.
No data showing the relationship between raccoon dogs and the virus were ever provided, even in the virologists’ report, hastily published after the media firestorm.
Some of the virologist coauthors peppered their statements to the press with caveats.
“We can’t definitively prove that there were infected raccoon dogs who were the first source of the virus going into humans,” Stephen Goldstein, a virologist at the University of Utah who worked on the analysis, told the Washington Post. “But it is highly suggestive of that.”
Other virologists were less careful.
“In samples with a hot amount of virus, there was not a trivial amount of DNA and RNA of raccoon dogs,” said Jeremy Kamil, an associate professor of microbiology and immunology at Louisiana State University Health Shreveport, in ABC News.
So what constitutes a “hot amount of virus?”
Raccoon dog redemption?
In late April, Jesse Bloom, a Fred Hutchinson Cancer Research Center virologist, published an independent analysis of both the the animal genetic data and the abundance of the virus in the samples.
Bloom’s reanalysis explored the environmental data more thoroughly than the China CDC paper or the Western virologists’ earlier report, painstakingly mapping the abundance of each species detected in the samples against the abundance of the virus.9
He found that the number of SARS-CoV-2 reads was not consistently correlated with any particular animal genetic material, and that the samples containing raccoon dog genetic material had some of the lowest reads of SARS-CoV-2.
Indeed the sample that had been the focus of so much media attention, Q61, had only a single read of SARS-CoV-2 out of 200 million reads in the sample.
A single molecule.
Of the other 13 samples with at least 20 percent of their genetic material coming from raccoon dogs, zero contained any virus.
Indeed, Bloom’s analysis revealed that raccoon dog genetic material was negatively correlated with SARS-CoV-2. The animals most strongly correlated with the virus in the seafood market? Various fish.
Needless to say, fish don’t spread SARS-CoV-2.
In the end, the analysis of SARS-CoV-2 and raccoon dog genetic material did not amount to much.
“Most commingling involves animals that definitely were not infected so it becomes impossible to ascribe any meaning to [a] small amount of commingling that could conceivably make sense,” Bloom said.
The findings corroborated a claim in the China CDC scientists’ original report: An intermediate host could not be inferred from this data.
Bloom stressed that the samples were swabbed too late to offer a snapshot of the moment the virus emerged in humans even if the pandemic did begin via spillover there.
The most generous interpretation of the raccoon dog report, the one proffered by Bloom, is that it provided a novel way to investigate which animals were present at the market10 but that it could not, as the authors had claimed, implicate raccoon dogs as the pandemic’s source.
Another interpretation of the Western virologists’ raccoon dog theory: They lied.
Did the omission of critical information about the amount of virus in the Q61 sample in their media blitz amount to intentional deception?11
It seems to me that the virologists behind the raccoon dog furor had, in a few hectic and monomaniacal days, believed that they had solved the origins of the pandemic.
Perhaps the data had the power to silence their critics on Twitter (and even stave off Congressional subpoenas). They didn’t pause to assess the full scope of the data and didn’t let the appeals from the Chinese scientists who had collected and uploaded the data delay them.
This sort of behavior is not characteristic of sober scientists.
Incomplete amends
My colleagues in the media, who are supposed to have honed expertise in detecting faulty claims, unearthing fraud, and calling out abuses of power — society’s professional bullshit detectors — have instead acted as accomplices.
Yesterday, The Atlantic ran a new story describing in blameless terms the fiasco it helped create.12
The Atlantic grilled Bloom with questions about obscure confounding variables in his analysis. (“How did the temperature of the fish stalls affect your analysis?”)
Yet in the earlier story, the raccoon dog team (which as you’ll recall, was led by two virologists under Congressional scrutiny for deception) were not asked more straightforward questions like: How much virus did you find in those samples? Why is there no data available for the public to see? Why are your findings in direct contradiction to the conclusions of the Chinese scientists who collected the data?
In the new Atlantic story we also hear from Felicia Goodrum, who until recently served as the president of the professional society for virologists.13 Goodrum, wouldn’t you know it, favors the theory that does not implicate virologists.
Not much of an amends to a story that has misled millions of people.
An artificial “consensus” in favor of a natural origin was built on lies in 2020 and little more than a molecule in 2023.
Perhaps the media has decided to simply embrace the warm glow of the bamboozle.
Footnotes:
Are references to Carl Sagan quotes hackish? Are David Foster Wallace-style footnotes hackish? I don’t know. I’m much more comfortable when I’m leaning on an inverted pyramid.
The Chinese scientists also shared their methodology for searching for traces of the virus in the wet market, which included a focus on the subset of stalls associated with early cases as well as the stalls that sold wildlife. Their paper directly challenges the claim by the Western virologists that a cluster of positive cases near those stalls shows that’s where the pandemic began, a key pillar of their argument in favor of a zoonotic origin. The Chinese scientists write: “Huanan Seafood Market was a large market with more than 600 stalls inside. Thus… early case-related stores and wildlife-related stores were prioritized for sample collection … Thus, it should be noted that these factors may lead to a biased sampling in the market.”
The Western virologists would later falsely claim that the China CDC denied that positive environmental samples contained animal genetic material. A Science report shows Western virologists were made aware of the existence of the presence of animal metadata in environmental samples by the China CDC preprint in the first place.
It should be noted for fairness that the Western virologists’ own claim that hospitalizations cluster around the wet market like a “bull’s-eye” relies on this same politically compromised WHO report, despite evidence from Chinese scientists and frontline doctors (suppressed by authorities but recovered by Gilles Demaneuf of DRASTIC) that this dataset is skewed and incomplete.
Chinese authorities’ quixotic search for the virus in sea life has come up empty.
Another high-profile media blitz about the wet market in 2022 followed an eerily similar pattern as the raccoon dog fiasco. In 2022, a team including Worobey, Andersen and Holmes claimed to have assembled dispositive evidence that the wet market was the unambiguous epicenter of the pandemic and therefore that “the lab leak theory is dead” in part using data pulled from the China CDC. Indeed, the Western team would have been unaware that the ancestral strain of SARS-CoV-2 was present at the market, a lynchpin of their argument, without their data. Some of the data from the China CDC preprint had been leaked to them, according to a podcast interview. That apparently enabled them to publish their preprint just hours after the China CDC went public with their own. Yet the Worobey team didn’t bother to acknowledge the completely contrary conclusions of the Chinese scientists, who argued that their data indicated that humans and not infected animals spread SARS-CoV-2 around the market. The Western virologists’ claims carried in the day in the Western mainstream press. The New York Times and CNN sent push alerts to millions of phones about their research. Few noticed the China CDC report or bothered to interview Gao. An approximate timeline of these events can be found here.
Gao has responded to the claim that they are aiding in a coverup of the illegal wildlife trade with disbelief, noting that there is already agreement that sort of trade was occurring at the wet market. “How can you hide something like this?” he asked me.
An exposé about GISAID published in Science soon after this fracas. I was told by a person familiar that it had been quickly moved off the back burner after GISAID embarrassed the world’s most influential virologists.
Bloom is an exceedingly polite rival to both Andersen and Worobey. In 2021, Andersen attempted to intimidate Bloom into not publishing a paper about sequences he recovered after Chinese scientists requested they be deleted, ostensibly because it would “fuel conspiratorial notions that China was hiding data.” Worobey accused Bloom of “stolen valor.” To my knowledge though, Bloom has never been locked out of a database for “unprecedented” disrespect for Chinese scientists. Bloom has never pointed out this hypocrisy.
The environmental data is nice confirmation, but was not necessary to prove this. The same team of virologists published pictures of raccoon dogs in the wet market in the winter of 2019 in their earlier 2022 report.
Though classified as a “positive” sample, sample Q61 had in fact tested negative for SARS-CoV-2 by PCR. China CDC’s manner of classifying positive and negative samples was not consistent, Bloom noted.
I’m being very hard on The Atlantic, but the New York Times deserves our jeers as well. Consider its coverage of the China CDC report, which as we’ve established, hypothesized that raccoon dogs could not be implicated in the pandemic’s origin, and that the wet market likely constituted a superspreader event. The New York Times’ headline about this study? “China Publishes Data Showing Raccoon Dog DNA at Wuhan Market.” Compare that to a recent presentation by Gao, and consider the dizzying spin happening at the paper of record.
Goodrum warned at a public hearing last year that new gain-of-function regulations could be “a solution looking for a problem.”
Relevant scientific publications:
Initial China CDC preprint (Gao et al.): https://www.researchsquare.com/article/rs-1370392/v1
Preprint claiming proof of wet market origin by Western virologists (Worobey et al.): https://zenodo.org/record/6299600
Revised peer reviewed wet market paper by Western virologists (Worobey et al.): https://www.science.org/doi/10.1126/science.abp8715
Revised peer reviewed China CDC paper (Liu et al.): https://www.nature.com/articles/s41586-023-06043-2_reference.pdf
The raccoon dog report: https://zenodo.org/record/7754299#.ZBomYuzML0o
The Bloom paper: https://www.biorxiv.org/content/10.1101/2023.04.25.538336v1
A partial picture of the rebuttals to Bloom:
https://threadreaderapp.com/thread/1651810509849542657.html
https://twitter.com/flodebarre/status/1652284507943231488?s=20