The raccoon dogs

Thousands of words have been devoted to analysing claims made in a recent report in The Atlantic – repeated in numerous other media outlets –that raccoon dogs being illegally sold at the Huanan market in Wuhan “could have been carrying and possibly shedding” SARS-CoV-2 at the end of 2019.

The author of the article in The Atlantic, Katherine Wu, said “experts” had told her that analysis of genetic sequences collected from the market was “some of the strongest support yet” that the Covid-19 pandemic began “when SARS-CoV-2 hopped from animals into humans, rather than in an accident among scientists experimenting with viruses”.

The co-author of the book ‘VIRAL: The Search for the Origin of Covid-19′, Matt Ridley, wrote in an article in The Spectator: “The claim is sadly what we ‘experts’ on this topic call a ‘grotesque exaggeration’.”

The new analysis was led by Kristian Andersen, virologist Edward Holmes from the University of Sydney, and Michael Worobey, an evolutionary biologist at the University of Arizona who hit the headlines in February 2022 when two studies he co-authored were published as preprints (‘The Huanan market was the epicenter of SARS-CoV-2 emergence’ and ‘SARS-CoV-2 emergence very likely resulted from at least two zoonotic events’, both published on February 26).

The sequences that have been grabbing media attention were spotted on the GISAID database by theoretician in evolutionary biology Florence Débarre, who works at the French national research agency, the CNRS. They were uploaded by Chinese researchers, but have since been removed (GISAID says this was at the request of the submitter). The genetic sequences were pulled out of swabs taken in and near market stalls “around the pandemic’s start”, Katherine Wu reported.

On March 14, several of the scientists involved in the new data analysis took part, along with researchers from China’s Center for Disease Control and Prevention, in a presentation of their analyses to members of the World Health Organisation’s Scientific Advisory Group for the Origins of Novel Pathogens (SAGO).

The WHO’s Covid-19 technical lead, Maria Van Kerkhove, said after the presentation: “We need to make clear that the virus has not been identified in an animal in the market or in animal samples from the market. Nor have we actually found the animals that infected humans. What this does is provides clues.”

Matt Ridley says he wrote in 2021 about raccoon dogs being on sale in the Huanan market. The sequences being vaunted as important new evidence show that raccoon dogs were in the market but not that they were infected with SARS-CoV-2, he says.

“Third,” he wrote, “the data behind the story are unavailable for inspection, having been deleted after they were briefly glimpsed by one scientist who appears to have grabbed them without permission of the author of those data.”

Richard Ebright tweeted: “It would be laughable that this is being portrayed as a revelation…except that it is not a mere joke, but, rather, an active disinformation campaign by knowingly and willfully complicit journalists.”

Ebright told Yahoo News reporter Alexander Nazaryan: “The data do not indicate that a raccoon dog was infected with SARS-CoV-2, much less that a raccoon dog was infected with SARS-CoV-2 and then transmitted SARS-CoV-2 to a human.”

Jamie Metzl told Nazaryan: “There is a zero percent chance that the evidence released so far constitutes a smoking gun proving a market origin of the pandemic. Anyone suggesting that this is the case is engaging in fraud.”

Alina Chan, who is the other co-author of ‘VIRAL: The Search for the Origin of Covid-19′, told Nazaryan that the data uploaded to GISAID didn’t distinguish whether the virus in the wildlife stall was brought there by a raccoon dog or by a person infected due to the superspreading in the market.

“It doesn’t even tell us if the raccoon dog was infected or if a surface contaminated by a sick person and the raccoon dog had been swabbed,” Chan was quoted as saying.

Chan is one of the scientists who has challenged Worobey’s argument that SARS-CoV-2 emerged from the Huanan market via zoonosis.

Worobey et al.’s preprints passed peer review and a new paper, ‘The Huanan Seafood Wholesale Market in Wuhan was the early epicenter of the Covid-19 pandemic’ was published in Science on July 26, 2022.

Alina Chan said in an article published on Medium that, after peer review, “unscientific language” was removed from the Worobey et al. manuscript.

Chan tweeted: “In order to argue for a market origin, Worobey and Pekar et al. had to (i) rule out the more likely scenario of a later infected case bringing the B variant to the market and (ii) explain why none of the early market cases had been infected with the A variant.

“This is why they came up with the 2 strains 2 spillover hypothesis, which stands on incredible shaky legs.”

Chan says in her Medium article that all of the observations that Worobey et al. cite as signs that the market was the outbreak epicenter “can be easily explained by the ascertainment bias with which early cases were identified”.

The papers co-authored by Worobey did not identify an animal at the Huanan seafood market that spread SARS-CoV-2 to humans.

The DRASTIC investigators stated in a report published in October 2022: “We find that the arguments by Worobey et al. that SARS-CoV-2 emerged from the Huanan seafood market via zoonosis and the hypothesis that at least two separate zoonotic jumps from wild animals occurred at the HSM are not supported by data.

“Consequently, we conclude the most likely scenario is that an infected person brought the virus to the HSM, sparking a superspreader event.”

In a preprint published on bioRxiv on October 13 Alex Washburne, Adrian Jones, Daoyu Zhang,  Yuri Deigin, Steven Quay, and Steven Massey state that the papers published in Science on July 26, 2022, by Worobey et al. and Pekar et al. were inconclusive as they failed to account for biases in how medical managers became alerted to SARS-CoV-2 and how public health authorities sampled early cases.

Washburne et al. say they used outbreak simulations to show that the findings of Pekar et al. were “heavily impacted by two methodological artifacts: the dubious exclusion of informative SARS-CoV-2 genomes, and their reliance on unrealistic phylodynamic models of SARS-CoV-2”.

In a Substack article entitled ‘Stop Shaming Raccoon Dogs’, published on March 19, Washburne writes: “From the same virologists who gave us the flawed, NIAID-prompted “Proximal Origin” piece, the flawed Pekar et al. analysis of early SARS-CoV-2 evolution, and the flawed Worobey et al. claim of “dispositive” evidence that seemed only to dispose of any future use of the word ‘dispositive’, we have another media blitzkrieg dropping bombs of over-hyped, under-performing work.”

Washburne added: We don’t have a peer-reviewed paper, we don’t even have a pre-print: we just have reports that some preliminary work was shared in a talk. We don’t even have the talk. In fact, we don’t even have the code or data used in the analysis. We have nothing more than a game of scientific telephone.

“Gao et al. uploaded a dataset, Proximal Origin authors stumbled upon this dataset “by pure happenstance”, ran a preliminary analysis, jumped at a finding that confirmed their biases, told the WHO SAGO about it, exploited their fame to tell the largest media outlets in the world about the preliminary analysis, and now RACCOON DOG is blaring on global megaphones with jumping headlines and overconfident language while the data that started this scientific Rube Goldberg machine has now conveniently disappeared.”

Washburne continued: “This episode is the most desperate, farcical episode in a series of increasingly outrageous, farcical episodes.

“These unjustified scientific media blitzes feel, to any reasoned skeptic … more like propaganda campaigns than diligent truth-digging efforts. These farces have turned The Atlantic, The New York Times, and The Guardian into the Three Stooges of SARS-CoV-2 origins reporting.”

Peter Daszak, meanwhile, continued to assert in a tweet on March 19: “Even the most plausible lab leak explanation has zero evidence for it.”

Regarding the raccoon dog sequences, he tweeted: “This level of scientific evidence is significant & very convincing, but undermined from day 1 by well-funded lab leak narrative from Miles Guo, Steve Bannon, the Republican Party, the Murdoch press, + 100s of sycophantic bloggers, podcasters, “truthers”, red pillers, & Qrazies.”

Two days after Katherine Hu’s article appeared in The Atlantic Worobey et al. published their report (‘Genetic evidence of susceptible wildlife in SARS-CoV-2 positive samples at the Huanan Wholesale Seafood Market, Wuhan: Analysis and interpretation of data released by the Chinese Center for Disease Control’) on zenodo.org.

The scientists wrote: “Our analysis of these data found that genetic evidence of multiple animal species was present in locations of the market where SARS-CoV-2 positive environmental samples had been collected.

“This includes raccoon dogs, which are susceptible to SARS-CoV-2 infection and shed sufficient virus to transmit to other species. However, this also included other mammalian species that require consideration as possible intermediate hosts of SARS-CoV-2.”

Worobey et al.’s paper was described as “explosive” by The Telegraph in Britain. Telegraph journalist Paul Nuki wrote: “The 19-strong international research team behind the analysis say the new data ‘contribute to and underscore the large body of evidence supporting a natural origin of SARS-CoV-2’.”

Other reactions to the paper’s publication were much more critical, however. Steven Massey analysed the paper in a detailed Twitter thread. He described Worobey et al.’s analysis as crude and said the “taxonomic attribution method” was naïve. “They rely on seq assembly, which miss a lot of info,” he tweeted.

Massey added: “Tellingly, none of the stalls with raccoon dog nuc acid have a human SARS2 case linked to it (which puzzlingly they fail to mention).”

The DRASTIC investigator who uses the Twitter handle @BillyBostickson, tweeted: “I get the impression that they repeatedly ‘filtered out’, ‘excluded’ and retained just enough data (based on possibly invalid data from China) to get the results they wanted to support their hypothesis!”

@BillyBostickson points to the funding that nine of the authors of the new paper have received from the NIH. The research project was itself financed in part with federal funds from the NIAID, the NIH, and the US Department of Health and Human Services.

A group of scientists from the NGO Biosafety Now have called on media outlets to “correct misleading articles about raccoon dogs starting the Covid-19 pandemic”. They include Richard Ebright; Colin Butler, who is the co-founder of the NGO the Benevolent Organisation for Development, Health and Insight (BODHI); neurobiologist Andre Goffinet; and Steven E. Phillips, MD, who specialises in the management of zoonotic infections.

The scientists said in a press release that the barrage of news reports that strongly hinted that the question of the origin of the Covid-19 pandemic had been solved were deeply misleading and should be corrected.

“We also believe the reports reflect yet another example of a small group of researchers exaggerating their findings and misleading the public with false certainty about the origins of Covid-19,” they added.

Matt Ridley tweeted: “Surely even @nytimes, @guardian, @TheAtlantic, @sciam, @ScienceMagazine and others must now realise how embarrassingly they were duped by some unscrupulous spin doctors over the raccoon dog non-story. An acutely embarrassing episode for such media.”

In an interview with John Yang of PBS (the Public Broadcasting Service) Katherine Hu makes clear her intention in writing her piece in The Atlantic.

UPDATE:

Florence Débarre tweeted on March 21 that she could no longer access GlSAlD  and it seemed that her co-authors could not access the database either.

GISAID issued a statement on March 21, giving its comments about “the speculations surrounding data availability”. It stated: “It is GISAID’s understanding that after the China CDC submitted a first draft of their analysis to a major scientific journal, a first peer-review process yielded the request for more and improved data. The China CDC complied and provided the reviewers with improved and additional sequence data as part of a manuscript currently under review.

“At the same time, some GISAID users accessed and downloaded an incomplete portion of these data. GISAID’s terms of use explicitly permit users to collaborate with other GISAID users on analyses of this data.

“However, if GISAID users were to publish an analysis of this un-published data before the data generators’ own publication is released (especially, if they had knowledge the data generators submitted their own manuscript for publication), such an act would amount to scooping.”

This, GISAID said, could not only could distort scientific progress, it could negatively impact the quality of scientific work.

“Unfortunately, GISAID learned that select users published an analysis report in direct contravention of the terms they agreed to as a condition to accessing the data, and despite having knowledge that the data generators are undergoing peer review assessment of their own publication,” GISAID added.

“When GISAID sought confirmation from the data generators whether best efforts to collaborate have been made in this case, GISAID was advised that a group of researchers contacted the data generators to communicate only their intent to publish their analysis of the generators’ data. As such, the best efforts requirement has not been met. GISAID communicated the above-stated observations to these users on 14 March 2023 and provided them with the opportunity to comment, but did not receive a reply as of this writing.”

GISAID added: “GISAID is confident that the peer-review by the scientific journal will be expedited to the extent possible. GISAID strongly encourages that the complete and updated dataset will be made available as soon as possible to all GISAID users.

“Premature discussions of the scientific data in the media risks eroding the public’s confidence in scientific research.”

Jesse Bloom, who uses the Twitter handle @jbloom_lab, posted a detailed thread on Twitter on March 22. “I’ve refrained from commenting on metagenomics of environmental samples from Huanan Seafood Market, since media coverage preceded description of data or analysis,” Bloom tweeted. “Data still not available, but there is now enough written down to offer partially informed assessment.”

Bloom tweeted that, overall, the “main thing we learn is details of which animals or products (eg, meats) were in market before it closed on Jan-1-2020”.

He added: “This doesn’t tell us if any infected w SARS2. But knowing more about animals could help trace supply chain, which is valuable line of investigation.”

Bloom said that human SARS-CoV-2 infections started in Wuhan no later than November 2019. “So we have to be circumspect about environmental samples from Jan 2020,” he tweeted.

“Eg, raccoon dog sample Q61 was collected on Jan-12-2020, which is at least 6 and probably >8 weeks after first human infections.”

UPDATE:

An unedited version of the much-heralded manuscript by William J. Liu (from the Chinese Centre for Disease Control and Prevention) et al., entitled ‘Surveillance of SARS-CoV-2 at the Huanan Seafood Market’ was published in Nature on April 5.

In the ‘Accelerated Article Preview’ Liu et al. state: “The origin of the virus cannot be determined from all the analyses available so far.

“Although gene barcode analysis of animal species in the study suggested that Myotis, Nyctereutes and Melogale – species that have been recognized as potential host species of sarbecoviruses – were present at the market, these barcodes were mostly detected within the SARS-CoV-2 PCR negative environment samples.

“It remains possible that the market may acted as an amplifier of transmission due to the high number of visitors every day, causing many of the initially identified infection clusters in the early stages of the outbreak.”

Liu et al. refer to the hypothesis in one of the two reports published by Michael Worobey and Jonathan Pekar et al. on February 26, 2022, that SARS-CoV-2 spilled over from animals to humans at least twice in November or December 2019, and the hypothesis that a raccoon dog was the intermediate host animal.

“The evidence provided in this study is not sufficient to support such a hypothesis,” Lui et al. said.

Lui et al. said their study confirmed the existence of raccoon dogs and other hypothesised/potential SARS-CoV-2 susceptible animals, at the market prior to its closure, but the environmental samples could not prove that the animals were infected.

“Furthermore, even if the animals were infected, our study does not rule out that human-to-animal transmission occurred, considering the sampling time was after the human infection within the market as reported retrospectively,” the researchers added.

Thus, Lui et al. said, the possibility of potential introduction of the virus to the market through infected humans or cold chain products could not be ruled out yet.

They added: “We should note that the selection of shops for sampling was biased because shops selling wildlife as well as shops linked to early cases were prioritized for sampling.”