Wuhan Market

COVID-origins data from Wuhan market published: what scientists think

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First peer-reviewed analysis of the Chinese swabs confirms animal DNA was present in samples that tested positive for SARS-CoV-2.

View of Wuhan Huanan Wholesale Seafood Market before its closure with meat carcasses hanging from vendors shop front
The now-closed Huanan Wholesale Seafood Market in Wuhan, China, is at the centre of the hypothesis that the SARS-CoV-2 virus ‘spilled over’ from animals to humans.

Researchers at the Chinese Center for Disease Control and Prevention (China CDC) have published an eagerly awaited analysis1 of swabs collected at a wet market in Wuhan, China, in the early weeks of the COVID-19 pandemic — as well as the underlying data, which the international research community has been calling for since the beginning of the outbreak.

The analysis, published in Nature on 5 April, confirms that swabs from the Huanan Seafood Wholesale Market — which closed in January 2020 and has long been linked to the start of the pandemic — contained genetic material from wild animals and tested positive for SARS-CoV-2. This suggests that it’s possible an animal could have been an intermediate host of a virus that spilled over to infect humans. But researchers say the latest findings still fall short of providing definitive proof that SARS-CoV-2 originated from an animal-to-human spillover event. (The study authors, led by former China CDC director George Gao, did not respond to requests for comment from Nature’s news team, which is editorially independent of Nature’s journal team.)COVID-origins report sparks debate over major genome hub GISAID

Still, researchers say that the publication of the genomic data, which have been deposited on open repositories, is crucial — because it will allow further analyses that could offer clues about the pandemic’s origin. “It’s one of the most important data sets we’ve had since the emergence of the pandemic,” says Florence Débarre, an evolutionary biologist at the French national research agency CNRS in Paris, who was part of a team that caused controversy by publishing its own analysis of the China CDC data last month. “They exist because at the time the right things were done.”

Evolutionary virologist Jesse Bloom says that although the swabs, which were collected in January 2020, provide useful information about what animals were at the market, even earlier samples are needed to find the pandemic’s origins. “If we ever learn the exact origins of SARS-CoV-2, I suspect it will come from new information about cases or events in early December or November of 2019, or earlier,” says Bloom, who is at the Fred Hutchinson Cancer Center in Seattle, Washington.

The paper is the latest in a series of published analyses of these market samples, and the first to be peer reviewed. The findings agree with a separate preprint analysis that the swabs contain genetic data from wild animals and from SARS-CoV-2. But these environmental samples do not confirm that any of the animals present were infected with the virus.

The Chinese team behind the latest report had published a preprint version2 of its study in February 2022 that did not include an analysis of animal genetic material in the swabs, and did not make public the underlying sequence data. The team that included Débarre found the China CDC swab data in the online genomics database GISAID and published its own analysis on the research repository Zenodo3. That report identified wild-animal material in the swabs that tested positive for SARS-CoV-2 and pointed to animals, including raccoon dogs, as species of interest.

Contentious study

The latest report lends weight to one of the two competing theories about how the COVID-19 pandemic began. Debate has raged over whether it had a natural origin, with a virus passing from animals to humans, or arose from a laboratory leak at the Wuhan Institute of Virology.

The Huanan market has been at the centre of the natural-origin theory because several of the earliest known cases of COVID-19 were linked to the market. Animals that were sold there are known to be hosts for respiratory viruses called sarbecoviruses, which include SARS-CoV-2. However, the lab-leak hypothesis gained momentum in 2021 and has not been definitively ruled out.

A raccoon dog seen behind the bars of a cage
Genetic material from raccoon dogs was present in samples that tested positive for SARS-CoV-2 that were taken from the Huanan market.

The latest paper, like the Zenodo report, contains details about mammalian genomic sequences present in the market samples. The authors analysed 60 samples that tested positive for SARS-CoV-2 — 11 more than in the Zenodo report — and a further 112 swabs that were negative.

The findings support the natural-origin hypothesis, says a researcher who was not involved in either study and wishes to remain anonymous owing to the controversy surrounding COVID-origins work. The presence of many wild-animal species means that a viral spillover that resulted in the COVID-19 pandemic could have occurred, says the scientist. Some of those species, such as raccoon dogs, have the potential to transmit SARS-CoV-2 infections, the source adds. “The extent of circumstantial evidence [in the latest paper] is greater than one can find for the alternate hypothesis, which is that it leaked from a laboratory.”COVID-origins study links raccoon dogs to Wuhan market: what scientists think

The study also offers clues about the role of the market in the pandemic’s origin. In the early weeks of the outbreak, two lineages of SARS-CoV-2 — dubbed A and B — were circulating. Initially, tests identified only lineage B at the market. This led some researchers to conclude that the market might have acted only as a site for an early ‘superspreader’ event, rather than as a site of an animal spillover, because lineage A is thought to be more ancestral.

But the China CDC’s preprint posted last year identified lineage A in one sample. “It’s the result that really made me shift, that made me really say, ‘OK, it’s very likely to come from the market,’” says Débarre. But she says that some questioned whether the result was real. The new analysis confirms the presence of lineage A, addressing those doubts, she says.

David Relman, a microbiologist at Stanford University in California, agrees with the authors’ assessment in the study that the market might have acted as an amplifier of SARS-CoV-2 transmission. “It’s just as possible that humans brought the virus into the market, as animals might have.”

Spurious findings

Alice Hughes, a conservation biologist at the University of Hong Kong, has concerns about the quality of the analysis. As well as genomic fragments from animals including raccoon dogs, Hughes says that the paper identifies genetic material from pandas, mole rats and chimpanzees. Given that killing a panda attracts the death sentence in China, “there is absolutely no way any trace of panda could possibly be in that market”, she says.

The strange results could be from laboratory contamination, or improper processing of the data that failed to weed out spurious species identifications, says Hughes. “We must be exceedingly careful with interpreting or putting too much faith in the paper.”

Débarre also questions aspects of the results. The China CDC authors used two genomic-analysis methods: one that searches through all available genes and genomes, and another that zeroes in on specific sequences in the mitochondrial genome. The whole-genome method detected only a few raccoon-dog sequences in a sample that was full of raccoon-dog nucleic acids, according to the Zenodo analysis and the China CDC’s mitochondrial genome analysis, says Débarre.

The data do not clearly point to a specific animal as an intermediate host that passed the virus onto humans. But the researcher who wished to remain anonymous says that the results again highlight some animals, including raccoon dogs, that can be studied for how well they transmit SARS-CoV-2.

Débarre says that further forensic analyses could reveal whether any animal DNA in the swabs bears signs of immune-system activation, which could indicate active infection. That could help to address concerns that the presence of virus and animal DNA in the same sample does not necessarily indicate that an animal was infected.

But Relman doesn’t think that further analyses of the same data set could lead to significant answers about the virus’s origin. “What we really need are other kinds of data. Good verifiable data on the early clinical events in Wuhan.”

source: Nature

New Studies Support Wuhan Market as Pandemic’s Origin Point

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The reports’ authors say that the novel coronavirus, or SARS-CoV-2, jumped from animals sold at the market to people twice in late 2019—but some scientists want more definitive evidence

New Studies Support Wuhan Market as Pandemic's Origin Point
View of Wuhan Huanan Wholesale Seafood Market before its closure in Hankou, Wuhan city, central China’s Hubei province, 31 December 2019. C

Scientists have released three studies that reveal intriguing new clues about how the COVID-19 pandemic started. Two of the reports trace the outbreak back to a massive market that sold live animals, among other goods, in Wuhan, China and a third suggests that the coronavirus SARS-CoV-2 spilled over from animals—possibly those sold at the market—into humans at least twice in November or December 2019. Posted on 25 and 26 February, all three are preprints, and so have not been published in a peer-reviewed journal.

These analyses add weight to original suspicions that the pandemic began at the Huanan Seafood Wholesale Market, which many of the people who were infected earliest with SARS-CoV-2 had visited. The preprints contain genetic analyses of coronavirus samples collected from the market and from people infected in December 2019 and January 2020, as well as geolocation analyses connecting these samples to a section of the market where live animals were sold. Taken together, these different lines of evidence point towards the market as the source of the outbreak—much like animal markets were ground zero for the severe acute respiratory syndrome (SARS) epidemic of 2002–2004—says Kristian Andersen, a virologist at the Scripps Research Institute in La Jolla, California, and an author on two of the reports. “This is extremely strong evidence,” he says.

Still, none of the studies contain definitive evidence about what type of animal might have harbored the virus before it spread to humans. Andersen speculates that the culprits could be raccoon dogs, a squat dog-like mammal used for food and for their fur in China. One of the studies he coauthored suggests that raccoon dogs were sold in a section of the market where several positive samples were collected. And reports show that the animals are capable of harboring other types of coronaviruses.ADVERTISEMENT

Some virologists say that the new evidence pointing to the Huanan market doesn’t rule out an alternative hypothesis. Namely, they say that the market could have just been the location of a massive amplifying event, in which an infected person spread the virus to many other people, rather than the place of the original spillover.

“Analysis-wise, this is excellent work, but it remains open to interpretation,” says Vincent Munster, a virologist at the Rocky Mountain Laboratories, a division of the National Institutes of Health, in Hamilton, Montana. He says searching for SARS-CoV-2 and antibodies against it in blood samples collected from animals sold at the market, and from people who sold animals at the market, could provide more definitive evidence of COVID-19’s origins. The number of positive samples from the market suggests an animal source, Munster says. But he is frustrated that more thorough investigations haven’t already been conducted: “We are talking about a pandemic that has upended the lives of so many people.”

GROUND ZERO?

In early January 2020, Chinese authorities identified the Huanan market as a potential source of a viral outbreak because the majority of people infected with COVID-19 at that time had been there in the days before they began to show symptoms, or were in contact with people who had. Hoping to stem the outbreak, Chinese authorities shuttered the market. Then researchers collected samples from poultry, snakes, badgers, giant salamanders, Siamese crocodiles and other animals sold there. They also swabbed drains, cages, toilets and vendor stalls in search of the pathogen. Following an investigation led by the World Health Organization (WHO), researchers released a report in March 2021 showing that all of the nearly 200 samples collected directly from animals were negative, but that more than 1,000 environmental samples from the stalls and other areas were positive.

A research team from China including the head of China’s Center for Disease Control and Prevention (CDC) has now genetically sequenced those positive samples, releasing the results in a preprint posted on 25 February. The scientists confirm that the samples contain SARS-CoV-2 sequences nearly identical to those that have been circulating in humans. Further, they show that the two original virus lineages circulating at the start of the pandemic, called A and B, were both present at the market.

“It’s a nice piece of work,” says Ray Yip, an epidemiologist who is a former director of the China branch of the US Centers for Disease Control and Prevention. “They’ve confirmed that the Huanan market was indeed a very important spreading location.”ADVERTISEMENT

As soon as the report from China posted online, Andersen and his colleagues rushed to post the manuscripts they had been working on for weeks.

In one, the team zeroed in on the southwestern section of the Huanan market, where live animals were sold as recently as 2019, as being the potential epicentre of the outbreak. They arrived at this conclusion by compiling information on the first known COVID-19 cases in China, as reported in various places, including the WHO investigation, newspaper articles, and from audio and video recordings of doctors and patients in Wuhan. This geospatial analysis found that 156 cases in December 2019 clustered tightly around the market and then gradually became more dispersed around Wuhan in January and February 2020.

They also examined the locations of the positive samples collected in the market, as reported in the WHO study, and fleshed out information about their potential surroundings by collecting business registration information, photographs of the market before it closed, and scientific reports that have emerged since the WHO’s investigation. For example, one paper published last year documented some 47,000 animals—including 31 protected species—sold in Wuhan markets between 2017 and 2019.

In one major finding in the new preprint, Andersen and colleagues mapped five positive samples from the market to a single stall that sold live animals, and more specifically to a metal cage, to carts used to move animals, and to a machine used to remove bird feathers. One of the coauthors on the report, virologist Eddie Holmes at the University of Sydney in Australia, had been to this stall in 2014 and snapped photographs—included in this study—of a live raccoon dog in a metal cage, stacked above crates of poultry, with the whole assembly sitting atop sewer drains. Notably, in the study from the China CDC, sewage at the market tested positive for SARS-CoV-2.

In a second report, Andersen and colleagues concluded that lineage A and lineage B of SARS-CoV-2 are too different from one another on a genetic level for one to have evolved into the other quickly in humans. Therefore, they suggest that the coronavirus must have evolved within non-human animals and that the two different lineages spread to humans separately. Because lineage B was the far more prevalent variety in January 2020, among other reasons, the authors suggest that it spilled over into humans before lineage A. Other outbreaks of coronaviruses, such as the SARS and Middle East respiratory syndrome (MERS) epidemics, also resulted from repeated introductions from wildlife, the paper notes.

Taking all of the new data together, and adding a degree of speculation, Andersen suggests that raccoon dogs could have been infected on a farm that then sold the animals at the markets in Wuhan in November or December 2019, and that the virus might have jumped to people handling them, or to buyers. At least twice, those infections could have spread from an index case to other people, he says.

‘AS GOOD AS IT GETS’

Over the past year, Michael Worobey, a virologist at the University of Arizona, in Tucson, and an author on the papers with Andersen says that his thinking on the origins of COVID-19 has shifted. Back in May 2021, he led a letter published in Science in which he and other researchers pressed the scientific community to keep an open mind about whether the pandemic stemmed from a laboratory, a controversial hypothesis suggesting that SARS-CoV-2 was either created in a lab, or was accidentally or intentionally released by researchers at the Wuhan Institute of Virology. “You want to take this kind of thing seriously,” he explains.

But since May, additional evidence has come to light that supports a zoonotic origin story similar to that of HIV, Zika virus, Ebola virus and multiple influenza viruses, he says. “When you look at all of the evidence, it is clear that this started at the market,” he says. Separate lines of analysis point to it, he says, and it’s extremely improbable that two distinct lineages of SARS-CoV-2 could have been derived from a laboratory and then coincidentally ended up at the market.

Nonetheless, Munster says he is not completely convinced of two spillover events because, alternatively, the virus might have evolved from one lineage into the other within a person who was immunocompromised. He adds that more data collected from people and animals is needed to answer this question, and to show that the first spillover occurred at the Huanan market. David Relman, a microbiologist at Stanford University in California, agrees that the preprints are not definitive, and that they exclude the possibility that people were infected prior to the outbreak at the market, but went undiagnosed.

Holmes fears that additional samples from early human cases and from animals might never materialize. Last July, for example, Chinese officials said that they planned to analyse patient blood samples from 2019, stored at the Wuhan Blood Centre—but if that study has been conducted, it has yet to be made public. “This is as good as it gets,” Holmes says. “What we should focus on now is trying to keep these events from happening again.”