China's secret raccoon dog evidence: What it means for the origin of Covid

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Almost all news outlets are talking about the latest evidence of Covid-19 origin, the natural origin in particular. But the lab leak camp remains unconvinced, and perhaps rightly so. 

Let’s see what both camps have to say and which side is more convincing. I used to remain neutral about both the lab leak and natural origin of Covid-19, as evident in a few of my prior work, but not now anymore. 

The raccoon dog evidence of Covid origin

In February 2022, Gao et al. from the Chinese Academy of Sciences and China Center for Disease Control and Prevention (CCDC) released a preprint of their study, which is still a preprint (not peer-reviewed) today. 

In this study, they tested 1,380 environmental and animal samples in the Wuhan wet market in early 2020, of which 73 environmental samples tested positive for SARS-CoV-2. Live SARS-CoV-2 was even culturable and isolated from some of the positive environmental samples. The positive samples also correlated with the abundance of human DNA, suggesting that humans contaminated the environment, or vice-versa. But none of the animal samples covering 18 species tested positive for SARS-CoV-2. 

But Gao et al. did not provide their raw data, until this month when they posted the raw data in Global Initiative on Sharing Avian Influenza Data (GISAID), an open-access genomic database for viruses. 

Luckily, western scientists happened to spot the raw data and analyze them, revealing that the positive environmental samples also had lots of animal DNA, mostly from a raccoon dog. 

“Because of how the samples were gathered, and because viruses can’t persist by themselves in the environment, the scientists think that their findings could indicate the presence of a coronavirus-infected raccoon dog in the spots where the swabs were taken,” journalist Katherine J. Wu, Ph.D., wrote for The Atlantic, who was also the first to break the news. 

A few days later, the western scientists, Crits-Christoph et al. from institutions across the U.S., France, Australia, Canada, Belgium, and the U.K., released their analysis as a preprint, which contained more details.

As shown in Figure 1, most of the SARS-CoV-2-positive environmental samples Gao et al. identified came from the west market side. This market side was also selling live animals, including raccoon dogs. And Crits-Christoph et al. detected high levels of raccoon dog DNA, co-localized with SARS-CoV-2 RNA, in 6 samples from 2 stalls taken from this market side. 

“Raccoon dog genetic material was abundant on a SARS-CoV-2 positive sample from a cart, and much more so than human genetic material from the same sample,” Crits-Christoph et al. wrote. “This finding supports photographic evidence of the presence of live raccoon dogs in this area” taken from 2019 (Figure 2).
Figure 1: Spatial distribution of mammalian mitochondrial DNA sequences found in SARS-CoV-2 positive samples at the Huanan market.Photo byGao et al. (2022)
Fig 2. Photos of raccoon dog and other wildlife animals being sold at the Wuhan wet market in 2019.Photo byWorobey et al. (2019)

Before this evidence came to light, raccoon dogs were already prime suspects of the intermediate host of SARS-CoV-2, mediating the spillover from bats to humans. This is because lab experiments showed that raccoon dogs can easily get infected with and transmit SARS-CoV-2. 

While other animals like mice, minks, and ferrets can catch and transmit SARS-CoV-2 in lab settings, SARS-CoV-2 had to undergo further adaptations and mutations for that to happen. Because such adaptations were not present in early variants of SARS-CoV-2, those animals are unlikely intermediate hosts of SARS-CoV-2. 

But raccoon dogs are special because SARS-CoV-2 need not adapt further to infect and spread from this animal, as writer The Gift Of Fire pointed out in January this year. This writer is arguably one of the, if not the, earliest to highlight raccoon dogs as the likely origin of Covid. 

In a separate article, The Gift Of Fire noted that raccoon dogs in the market also carried live SARS viruses back in 2003. Indeed, a 2007 research review identified raccoon dogs as the next most susceptible species to SARS (after civets) out of the 29 animals examined (Figure 3). 

17 years went by, and as a result of China’s negligence in regulating wildlife trade, the world is in danger.
Fig 3: Summary of investigations of SARS-CoV-1 in animal species other than civets. The bottom half of the table continues in the paper.Photo byShi and Zhu (2007)

What it means for the origin of Covid

As you might have realized, just finding the genetic materials of raccoon dogs and SARS-CoV-2 co-localizing in the same stall that sold raccoon dogs isn’t definitive proof of Covid origin. Many remain unconvinced. 

The new data “doesn’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,” Alina Chan, a molecular biologist at the Broad Institute of MIT and Harvard, told Yahoo News. “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.”

But objectively speaking, it’s more likely that raccoon dogs contaminated the environmental sample (i.e., the cart), not humans. Far more raccoon dog DNA was identified from the SARS-CoV-2-positive cart than human DNA. As viruses can’t survive without a host, they can’t persist in the environment alone. Now, which host was more likely to harbor SARS-CoV-2 in the cart sample? The abundant raccoon dog DNA or minuscule human DNA? If I have to bet money, obviously I’ll bet on the former. 

“Still, the evidence falls short of, say, isolating SARS-CoV-2 from a free-ranging raccoon dog or, even better, uncovering a viral sample swabbed from a mammal for sale at Huanan from the time of the outbreak’s onset,” Wu also admitted. “That would be the virological equivalent of catching a culprit red-handed.” With the current evidence, it’s similar to “finding the DNA of an investigation’s main suspect at the scene of the crime.”

In other words, SARS-CoV-2-positive animal samples are still the missing evidence to prove the wet market origin of Covid. 

For instance, to prove the wet market origin of SARS-CoV-1, live viruses with 99.8% similarity to human SARS were found in civets in the market. That’s sufficient proof. It’s impossible to go back in time to witness the exact sequence of spillover of SARS, Covid, or other viruses. 

But finding such proof is too late because all live animals from the market were removed and presumably killed even before investigations into the origin were conducted. Unless a miracle happens, you can’t restore what was destroyed, including evidence. 

The raccoon dog evidence is, therefore, the only concrete evidence we have on the origin of Covid, which is why The Atlantic called it “the strongest evidence yet.” All the prior evidence, including the lab leak, was just circumstantial evidence that’s up to the individual to interpret. So when push comes to shove, the natural origin of Covid wins. 

(For a rundown of the prominent lab leak theories, including the infamous DEFUSE grant proposal and furin cleavage site, The Gift Of Fire has done a brilliant job in addressing them here.)

China has been hiding evidence

But why is it only now that the raccoon dog evidence appears, even when Gao et al. released the preprint in February last year? Either China’s scientists overlooked the evidence or tried to hide it. 

In Gao et al.’s preprint, they tested 457 animal samples from over 20 species for SARS-CoV-2 and none were positive. This isn’t surprising because none of the animal samples tested belonged to raccoon dogs. As mentioned, those raccoon dogs were probably culled before any investigations were made. Fair enough.

But in the graphic depicting the metagenomic analysis showing the correlation between SARS-CoV-2-positive environmental samples and human DNA, many dots in the graphic were unlabeled and belonged to species other than humans (Figure 4). But Gao et al. did not specify the species and were suspected of ignoring the animal evidence to push the narrative that humans outside the market brought the virus in.
Fig 4: Correlation of SARS-COV-2 with other species (unspecified) in SARS-CoV-2-positive environmental cases.Photo byGao et al. (2022)

It’s also suspicious that Gao et al. or the CCDC scientists hold on to their raw data for years. Only recently did they quietly upload the raw data on GISAID, as a requirement from the journal they are trying to publish their preprint in. Upon request, the CCDC scientists permitted Crits-Christoph et al. to analyze the raw data. But shortly after Crits-Christoph et al. analyzed and communicated their findings, the raw data disappeared from GISAID without any explanation. Crits-Christoph et al. were even accused of breaching ethics by using someone else’s raw data. 

Unfortunately, Crits-Christoph et al. did not manage to retrieve all the raw data. Their analyses were only based on partial data from a subset of SARS-CoV-2-positive environmental samples from the wet market.

“Additional data also exist for the remaining SARS-CoV-2 positive samples, as well as for other environmental samples from the Huanan market that were negative for SARS-CoV-2. These data have not yet been shared, precluding further analysis,” Crits-Christoph et al. wrote. “All of these missing data could provide valuable information on the timeline of events at the Huanan market and the provenance of the virus.”

“These data could have — and should have — been shared 3 years ago,” said the WHO Director-General, Tedros Adhanom Ghebreyesus.

China is hiding the raccoon dog or animal evidence presumably because they don’t want to be held responsible for initiating a global pandemic. China has been denying that Covid came from this country for years, even going as far as claiming that Covid originated from an army lab in the U.S. or imported frozen foods, among other things, to avoid blame.

Initially, China also denied that live animals were sold in the wet market in 2019. But in an ironic act of China’s own scientists, a 2021 published study detailed animal sales from the wet market, of which raccoon dogs were among the most prized items. And the wild animals were kept in poor hygienic conditions, conducive to zoonotic infections, the study described. 

Like vaccine safety, Covid-19 origin has also become a highly polarizing topic with sides of lab leak or natural origins. And the lab leak story will persist because it’s simply more exciting and some people desperately want it to be true for political or monetary reasons. It's just anti-climatic if one of the deadliest pandemics in history is just like any other zoonotic infection, i.e., spillover from animals.

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MSc Biology | 9x first-author academic papers | 280+ articles on coronavirus | Independent science writer


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