{"id":2941,"date":"2023-03-16T05:15:54","date_gmt":"2023-03-16T10:15:54","guid":{"rendered":"https:\/\/www.unmc.edu\/healthsecurity\/transmission\/?p=2941"},"modified":"2026-02-11T13:17:23","modified_gmt":"2026-02-11T19:17:23","slug":"the-strongest-evidence-yet-that-an-animal-started-the-pandemic","status":"publish","type":"post","link":"https:\/\/www.unmc.edu\/healthsecurity\/transmission\/2023\/03\/16\/the-strongest-evidence-yet-that-an-animal-started-the-pandemic\/","title":{"rendered":"The Strongest Evidence Yet That an Animal Started the Pandemic"},"content":{"rendered":"
\n

The Atlantic<\/a> A new analysis of genetic samples from China appears to link the pandemic\u2019s origin to raccoon dogs. For three years now, the debate over the origins of the coronavirus pandemic has ping-ponged between two big ideas: that SARS-CoV-2 spilled into human populations directly from a wild-animal source, and that the pathogen leaked from a lab. Through a swirl of data obfuscation by Chinese authorities and politicalization within the United States, and rampant speculation from all corners of the world, many scientists have stood by the notion that this outbreak\u2014like most others<\/a>\u2014had purely natural roots. But that hypothesis has been missing a key piece of proof: genetic evidence from the Huanan Seafood Wholesale Market in Wuhan, China, showing that the virus had infected creatures for sale there. <\/p>\n\n\n\n

Now, an international team of virologists, genomicists, and evolutionary biologists may have finally found crucial data to help fill that knowledge gap. A new analysis of genetic sequences collected from the market shows that raccoon dogs being illegally sold at the venue could have been carrying and possibly shedding the virus at the end of 2019. It\u2019s some of the strongest support yet, experts told me, that the pandemic began when SARS-CoV-2 hopped from animals into humans, rather than in an accident among scientists experimenting with viruses.

\u201cThis really strengthens the case for a natural origin,\u201d says Seema Lakdawala, a virologist at Emory University who wasn\u2019t involved in the research. Angela Rasmussen, a virologist involved in the research, told me, \u201cThis is a really strong indication that animals at the market were infected. There\u2019s really no other explanation that makes any sense.\u201d<\/p>\n\n\n\n

The findings won\u2019t fully convince the entrenched voices on either side of the origins debate. But the new analysis may offer some of the clearest and most compelling evidence that the world will ever<\/em> get in support of an animal origin for the virus that, in just over three years, has killed nearly 7 million people<\/a> worldwide.<\/p>\n\n\n\n

The genetic sequences were pulled out of swabs taken in and near market stalls around the pandemic\u2019s start. They represent the first bits of raw data that researchers outside of China\u2019s academic institutions and their direct collaborators have had access to. A few weeks ago, the data appeared on an open-access genomic database called GISAID, after being quietly posted by researchers affiliated with the country\u2019s Center for Disease Control and Prevention. By almost pure happenstance, scientists in Europe, North America, and Australia spotted the sequences, downloaded them, and began an analysis.<\/p>\n\n\n\n

The samples were already known to be positive for the coronavirus, and had been scrutinized before<\/a> by the same group of Chinese researchers who uploaded the data to GISAID. But that prior analysis, released as a preprint publication in February 2022, asserted that \u201cno animal host of SARS-CoV-2 can be deduced.\u201d Any motes of coronavirus at the market, the study suggested, had most likely been chauffeured in by infected humans, rather than wild creatures for sale.<\/p>\n\n\n\n

The new analysis, led by Kristian Andersen, Edward Holmes, and Michael Worobey\u2014three prominent researchers who have been looking into the virus\u2019s roots\u2014shows that that may not be the case. 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\u2014much of which was a match for the common raccoon dog, a small animal related to foxes that has a raccoon-like face. Because of how the samples were gathered, and because viruses can\u2019t 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. Unlike many of the other points of discussion that have been volleyed about in the origins debate, the genetic data are \u201ctangible,\u201d Alex Crits-Christoph, a computational biologist and one of the scientists who worked on the new analysis, told me. \u201cAnd this is the species that everyone has been talking about.\u201d<\/p>\n\n\n\n

Finding the genetic material of virus and mammal so closely co-mingled\u2014enough to be extracted out of a single swab\u2014isn\u2019t perfect proof, Lakdawala told me. \u201cIt\u2019s an important step; I\u2019m not going to diminish that,\u201d she said. 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\u2019s onset<\/a>. That would be the virological equivalent of catching a culprit red-handed. But \u201cyou can never go back in time and capture those animals,\u201d says Gigi Gronvall, a senior scholar at the Johns Hopkins Center for Health Security. And to researchers\u2019 knowledge, \u201craccoon dogs were not tested at the market and had likely been removed prior to the authorities coming in,\u201d Andersen wrote to me in an email. He underscored that the findings, although an important addition, are not \u201cdirect evidence of infected raccoon dogs at the market.\u201d<\/p>\n\n\n\n

Still, the findings don\u2019t stand alone. \u201cDo I believe there were infected animals at the market? Yes, I do,\u201d Andersen told me. \u201cDoes this new data add to that evidence base? Yes.\u201d The new analysis builds on extensive previous<\/a> research<\/a> that points to the market as the source of the earliest major outbreak of SARS-CoV-2: Many of the earliest known COVID-19 cases of the pandemic were clustered roughly in the market\u2019s vicinity. And the virus\u2019s genetic material was found in many samples swabbed<\/a> from carts and animal-processing equipment at the venue, as well as parts of nearby infrastructure, such as storehouses, sewage wells, and water drains. Raccoon dogs, creatures commonly bred for sale in China, are also already known to be one of many mammal species that can easily catch and spread the coronavirus. All of this left one main hole in the puzzle to fill: clear-cut evidence that raccoon dogs and the virus were in the exact same spot at the market, close enough that the creatures might have been infected and, possibly, infectious. That\u2019s what the new analysis provides. Think of it as finding the DNA of an investigation\u2019s main suspect at the scene of the crime.<\/p>\n\n\n\n

The findings don\u2019t rule out the possibility that other animals may have been carrying SARS-CoV-2 at Huanan. Raccoon dogs, if they were infected, may not even be the creatures who passed the pathogen on to us. Which means the search for the virus\u2019s many wild hosts will need to plod on. \u201cDo we know the intermediate host was raccoon dogs? No,\u201d Andersen wrote to me, using the term for an animal that can ferry a pathogen between other species. \u201cIs it high up on my list of potential hosts? Yes, but it\u2019s definitely not the only one.\u201d<\/p>\n\n\n\n

On Tuesday, the researchers presented their findings at a hastily scheduled meeting of the World Health Organization\u2019s Scientific Advisory Group for the Origins of Novel Pathogens, which was also attended by several of the Chinese researchers responsible for the original analysis, according to multiple researchers who were not present but were briefed about it before and after by multiple people who were there. Shortly after the meeting, the Chinese team\u2019s preprint went into review at a Nature Research journal\u2014suggesting that a new version was being prepared for publication.<\/p>\n\n\n\n

At this point, it\u2019s still unclear why the sequences were so recently posted to GISAID. They also vanished from the database shortly after the international team of researchers notified the Chinese researchers of their preliminary findings, without explanation. When I emailed George Gao, the former China CDC director-general and the lead author on the original Chinese analysis, asking for his team\u2019s rationale, I didn\u2019t immediately receive a response\u2014though he later told Jon Cohen at Science<\/em> magazine<\/a> that this latest analysis represent \u201cnothing new.\u201d Given what was in the GISAID data, it does seem that raccoon dogs could have been introduced into and clarified the origins narrative far sooner\u2014at least a year ago, and likely more. On Friday, at a press briefing, Tedros Adhanom Ghebreyesus, WHO\u2019s director general, addressed the disappearing data, as well as the extreme lag with which it was posted to GISAID in the first place. \u201cThese data could have and should have been shared three years ago,\u201d he told reporters. \u201cWe continue to call on China to be transparent in sharing data and to conduct the necessary investigations to share the results.\u201d Maria Van Kerkhove, WHO\u2019s COVID-19 technical lead, also told me that the rapid unfolding of these events \u201cis an indication to me in recent days that there is more data that exists\u201d that could further clarify the pandemic\u2019s origins. And if that\u2019s the case, those data, especially any that speak to what has unfolded within China\u2019s borders, need \u201cto be made available immediately.\u201d<\/p>\n\n\n\n

China has, for years, been keen on pushing the narrative that the pandemic didn\u2019t start within its borders. In early 2020, a Chinese official suggested that the novel coronavirus may have emerged from a U.S. Army lab in Maryland. The notion that a dangerous virus sprang out from wet-market mammals echoed the beginnings of the SARS-CoV-1 epidemic two decades ago\u2014and this time, officials immediately shut down the Huanan market, and vehemently pushed back<\/a> against assertions<\/a> that live animals being sold illegally in the country were to blame; a WHO investigation in March 2021 took the same line<\/a>. \u201cNo verified reports of live mammals being sold around 2019 were found,\u201d the report stated. But just three months later, in June 2021, a team of researchers published a study<\/a> documenting tens of thousands of mammals for sale in wet markets in Wuhan between 2017 and late 2019, including at Huanan. The animals were kept in largely illegal, cramped, and unhygienic settings\u2014conditions conducive to viral transmission\u2014and among them were more than 1,000 raccoon dogs<\/a>. Holmes himself had been at the market in 2014<\/a> and snapped a photo at Stall 29, clearly showing a raccoon dog in a cage; another set of images from the venue, captured by a local in December 2019 and later shared on Weibo<\/a>, caught the animals on film as well\u2014right around the time that the first recorded SARS-CoV-2 infections in humans occurred.<\/p>\n\n\n\n

And yet, Chinese researchers maintained their stance. As Cohen reported last year<\/a>, scientists from several of China\u2019s largest academic institutions posted a preprint in September 2021 concluding that a massive nationwide survey of bats<\/a>\u2014the likeliest original source of the coronavirus before it jumped into an intermediate host, such as raccoon dogs, and then into us\u2014had turned up no relatives of SARS-CoV-2. The implication, the team behind the paper asserted, was that relatives of the coronavirus were \u201cextremely rare\u201d in the region, making it unlikely that the pandemic had started there. The findings directly<\/a> contradicted<\/a> others showing that cousins of SARS-CoV-2 were indeed circulating in China\u2019s bats. (Local bats have also been found to harbor viruses related to SARS-CoV-1<\/a>.)<\/p>\n\n\n\n

The original Chinese analysis<\/a> of the Huanan market swabs, from February 2022, also stuck with China\u2019s party line on the pandemic. One of the report\u2019s graphs suggested that viral material at the market had been mixed up with genetic material of multiple <\/em>animal species\u2014a data trail that should have led to further inquiry or conclusions, but that the Chinese researchers appear to have ignored. Their report noted only humans as being linked to SARS-CoV-2, stating that its findings \u201chighly\u201d suggested that any viral material at the market came from people (at least one of whom, presumably, picked it up elsewhere and ferried it into the venue). The Huanan market, the study\u2019s authors wrote, \u201cmight have acted as an amplifier\u201d for the epidemic. But \u201cmore work involving international coordination\u201d would be needed to suss out the \u201creal origins of SARS-CoV-2.\u201d<\/p>\n\n\n\n

The wording of that report baffled many scientists in Europe, North America, and Australia, several of whom had, almost exactly 24 hours after the release of the China CDC preprint, published early<\/a> versions<\/a> of their own<\/a> studies<\/a>, concluding that the Huanan market was the pandemic\u2019s probable epicenter\u2014and that SARS-CoV-2 might have made its hop into humans from the venue twice <\/em>at the end of 2019. Itching to get their hands on China CDC\u2019s raw data<\/a>, some of the researchers took to regularly trawling GISAID, occasionally at odd hours. Last Thursday evening, after spotting the sequences, Florence D\u00e9barre, an evolutionary biologist at the French National Centre for Scientific Research, alerted her colleagues about their availability. Stumbling across the data, which she was not expecting to pop up, was \u201ca total surprise,\u201d D\u00e9barre told me.<\/p>\n\n\n\n

Within hours of downloading the data and starting their own analysis, the researchers found their suspicions confirmed. Several surfaces in and around one stall at the market, including a cart and a defeathering machine, produced virus-positive samples that also contained genetic material from raccoon dogs\u2014in a couple of cases, at higher concentrations than of human genomes. It was Stall 29\u2014the same spot where Holmes had snapped the photo of the raccoon dog, nearly a decade before.<\/p>\n\n\n\n

Slam-dunk evidence for a raccoon-dog host\u2014or another animal\u2014could still emerge. In the hunt for the wild source of MERS, another coronavirus that caused a deadly outbreak in 2012, researchers were eventually able to identify the pathogen in camels<\/a>, which are thought to have caught their initial infection from bats<\/a>\u2014and which still harbor the virus today; a similar story has played out for Nipah virus<\/a>, which hopscotched<\/a> from bats to pigs to us<\/a>.<\/p>\n\n\n\n

Proof of that caliber, though, may never turn up for SARS-CoV-2. (Nailing wild origins is rarely simple: Despite a years-long search, the wild host for Ebola still has not been definitively pinpointed.) Which leaves just enough ambiguity to keep debate about the pandemic\u2019s origins running, potentially indefinitely. Skeptics will likely be eager to poke holes in the team\u2019s new findings\u2014pointing out, for instance, that it\u2019s technically possible for genetic material from viruses and animals to end up sloshed together in the environment even if an infection didn\u2019t take place. Maybe an infected human visited the market and inadvertently deposited viral RNA near an animal\u2019s crate.<\/p>\n\n\n\n

But an infected animal, with no third-party contamination, still seems by far the most plausible explanation for the samples\u2019 genetic contents, several experts told me; other scenarios require contortions of logic and, more important, additional proof. Even prior to the reveal of the new data, Gronvall told me, \u201cI think the evidence is actually more sturdy for COVID than it is for many others.\u201d The strength of the data might even, in at least one way, best what\u2019s available for SARS-CoV-1: Although scientists have isolated SARS-CoV-1-like <\/em>viruses<\/a> from a wet-market-traded mammal host, the palm civet, those samples were taken months after the outbreak began\u2014and the viral variants found weren\u2019t exactly identical<\/a> to the ones in human patients. The versions of SARS-CoV-2 tugged out of several Huanan-market samples, meanwhile, are a dead ringer<\/a> for the ones that sickened humans with COVID early on.<\/p>\n\n\n\n

The debate over SARS-CoV-2\u2019s origins has raged for nearly as long as the pandemic itself\u2014outlasting lockdowns, widespread masking, even the first version of the COVID vaccines. And as long as there is murkiness to cling to, it may never fully resolve. While evidence for an animal spillover has mounted over time, so too have questions<\/a> about the possibility that the virus escaped from a laboratory. When President Joe Biden asked the U.S. intelligence community to review the matter, four government agencies and the National Intelligence Council pointed to a natural origin<\/a>, while two others guessed that it was a lab leak. (None of these assessments were made with high confidence; a bill passed in both the House and the Senate<\/a> would, 90 days after it becomes a law, require the Biden administration to declassify underlying intelligence.)<\/p>\n\n\n\n

If this new level of scientific evidence does conclusively tip the origins debate toward the animal route, it will be, in one way, a major letdown. It will mean that SARS-CoV-2 breached our borders because we once again mismanaged our relationship with wildlife\u2014that we failed to prevent this epidemic for the same reason we failed, and could fail again, to prevent so many of the rest.<\/p>\n\n\n\n

This article originally stated that the raw data appeared on GISAID late last week. In fact, some of the data appeared even earlier.<\/em><\/p>\n

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The Atlantic A new analysis of genetic samples from China appears to link the pandemic\u2019s origin to raccoon dogs. For three years now, the debate over the origins of the coronavirus pandemic has ping-ponged between two big ideas: that SARS-CoV-2 spilled into human populations directly from a wild-animal source, and that the pathogen leaked from […]<\/p>\n","protected":false},"author":11,"featured_media":2945,"comment_status":"open","ping_status":"closed","sticky":false,"template":"","format":"standard","meta":{"_jetpack_memberships_contains_paid_content":false,"footnotes":"","jetpack_publicize_message":"","jetpack_publicize_feature_enabled":false,"jetpack_social_post_already_shared":false,"jetpack_social_options":{"image_generator_settings":{"template":"highway","default_image_id":0,"font":"","enabled":false},"version":2}},"categories":[11,7,21],"tags":[],"class_list":["post-2941","post","type-post","status-publish","format-standard","has-post-thumbnail","hentry","category-covid","category-emerging-infectious-diseases","category-featured"],"jetpack_publicize_connections":[],"jetpack_featured_media_url":"https:\/\/www.unmc.edu\/healthsecurity\/transmission\/wp-content\/uploads\/2023\/03\/Screenshot-2023-03-22-at-06.43.20.png","jetpack_sharing_enabled":true,"_links":{"self":[{"href":"https:\/\/www.unmc.edu\/healthsecurity\/transmission\/wp-json\/wp\/v2\/posts\/2941","targetHints":{"allow":["GET"]}}],"collection":[{"href":"https:\/\/www.unmc.edu\/healthsecurity\/transmission\/wp-json\/wp\/v2\/posts"}],"about":[{"href":"https:\/\/www.unmc.edu\/healthsecurity\/transmission\/wp-json\/wp\/v2\/types\/post"}],"author":[{"embeddable":true,"href":"https:\/\/www.unmc.edu\/healthsecurity\/transmission\/wp-json\/wp\/v2\/users\/11"}],"replies":[{"embeddable":true,"href":"https:\/\/www.unmc.edu\/healthsecurity\/transmission\/wp-json\/wp\/v2\/comments?post=2941"}],"version-history":[{"count":4,"href":"https:\/\/www.unmc.edu\/healthsecurity\/transmission\/wp-json\/wp\/v2\/posts\/2941\/revisions"}],"predecessor-version":[{"id":11403,"href":"https:\/\/www.unmc.edu\/healthsecurity\/transmission\/wp-json\/wp\/v2\/posts\/2941\/revisions\/11403"}],"wp:featuredmedia":[{"embeddable":true,"href":"https:\/\/www.unmc.edu\/healthsecurity\/transmission\/wp-json\/wp\/v2\/media\/2945"}],"wp:attachment":[{"href":"https:\/\/www.unmc.edu\/healthsecurity\/transmission\/wp-json\/wp\/v2\/media?parent=2941"}],"wp:term":[{"taxonomy":"category","embeddable":true,"href":"https:\/\/www.unmc.edu\/healthsecurity\/transmission\/wp-json\/wp\/v2\/categories?post=2941"},{"taxonomy":"post_tag","embeddable":true,"href":"https:\/\/www.unmc.edu\/healthsecurity\/transmission\/wp-json\/wp\/v2\/tags?post=2941"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}