{"id":2927,"date":"2023-03-21T20:52:47","date_gmt":"2023-03-22T01:52:47","guid":{"rendered":"https:\/\/www.unmc.edu\/healthsecurity\/transmission\/?p=2927"},"modified":"2023-03-22T05:52:23","modified_gmt":"2023-03-22T10:52:23","slug":"covid-origins-study-links-raccoon-dogs-to-wuhan-market-what-scientists-think","status":"publish","type":"post","link":"https:\/\/www.unmc.edu\/healthsecurity\/transmission\/2023\/03\/21\/covid-origins-study-links-raccoon-dogs-to-wuhan-market-what-scientists-think\/","title":{"rendered":"COVID-origins study links raccoon dogs to Wuhan market: what scientists think"},"content":{"rendered":"
\n

Nature<\/a> Some scientists say the analysis provides new evidence supporting the hypothesis that the virus that causes COVID-19 spilled over from an animal \u2014 but falls short of definitive proof.<\/strong><\/p>\n\n\n\n

Raccoon dogs, bamboo rats, palm civets: these are just some of the animals whose DNA has been found in swabs taken from the Huanan Seafood Wholesale Market in Wuhan, China, which has been linked to the origin of the COVID-19 pandemic. The swabs also tested positive for SARS-CoV-2, which causes the disease. The analysis \u2014 posted on 20 March to the research repository Zenodo1<\/a><\/sup> \u2014 provides evidence supporting the hypothesis that SARS-CoV-2 spilled over from animals to humans at the market, say some researchers.<\/p>\n\n\n\n

\u201cOf course, this is not direct evidence,\u201d says Leo Poon, a virologist at the University of Hong Kong, \u201cbut this is the best we can get now, because all the animals have been eliminated from the market and we don\u2019t have swabs of the animals.\u201d<\/p>\n\n\n\n

On 16 March, The Atlantic<\/em> first reported on the analysis<\/a>. The Zenodo posting, which has not been peer reviewed, is the first time that the full work has been released publicly \u2014 which could pave the way for follow-up studies, such as an investigation of where the animals in the market came from.<\/p>\n\n\n\n

The swabs were collected in early 2020, after the market was shut down and cleared of animal products.<\/p>\n\n\n\n

The researchers were specifically interested in looking for evidence of mammals, which could have been intermediate hosts of the virus. They identified near-complete mitochondrial DNA sequences \u2014 some 16,000-base-pairs long \u2014 for five species of wildlife, including raccoon dog (Nyctereutes procyonoides<\/em>), Malayan porcupine (Hystrix brachyura<\/em>), Amur hedgehog (Erinaceus amurensis<\/em>), masked palm civet (Paguma larvata<\/em>) and hoary bamboo rat (Rhizomys pruinosus<\/em>). \u201cIt\u2019s remarkable to have a list,\u201d says study co-author Alex Crits-Christoph, who is a computational biologist at a non-profit organization, and is based in Baltimore, Maryland.<\/p>\n\n\n\n

Particularly notable was the raccoon dog mitochondrial DNA found in six samples from two stalls. Research has shown that raccoon dogs \u2014 small fox-like animals \u2014 are susceptible to SARS-CoV-2, and can spread the infection to other raccoon dogs without showing clear signs of sickness. Raccoon dogs and masked palm civets have also been found with infections of viruses that are almost identical to the one that causes severe acute respiratory syndrome (SARS), which is related to SARS-CoV-2 and caused an outbreak in people in 2003. And work in palm-civet cells indicates that the creatures could possibly become infected with SARS-CoV-2.<\/p>\n\n\n\n

Studies suggest that a progenitor of SARS-CoV-2 probably originated in bats, but how it passed from bats to people is not clear. Scientists suspect an intermediate host was involved, but they have not found strong evidence, which has led to speculation that the virus could have instead leaked \u2014 deliberately or accidentally \u2014 from a laboratory in Wuhan.<\/p>\n\n\n\n

The new study does not confirm whether the animals themselves were infected with the virus. But establishing that the animals were present at the market supports the hypothesis that the pandemic had an animal origin, say some researchers.<\/p>\n\n\n\n

The information could be used to track where the animals in the market came from, which could inform efforts to understand the pandemic\u2019s start.<\/p>\n\n\n\n

Others are more cautious about drawing conclusions on the origins of the pandemic from the analysis. The work confirms which animal species were at the market, but because it includes only samples that had tested positive, \u201cthere is no data in this work associating SARS-CoV-2 with the presence of any of these animals\u201d, says Justin Kinney, a quantitative biologist at Cold Spring Harbor Laboratory in New York.<\/p>\n\n\n\n

\u201cThese data do not provide a definitive answer to the question of how the pandemic began,\u201d said Tedros Adhanom Ghebreyesus, director-general of the World Health Organization (WHO), at a press event on 17 March, after he had been briefed in advance of the report\u2019s release. \u201cBut every piece of data is important in moving us closer to that answer,\u201d he said.<\/p>\n\n\n\n

Appearance and disappearance<\/strong><\/h2>\n\n\n\n

The swabs were originally referred to in a preprint paper by George Gao2<\/a><\/sup>, former director of the Chinese Center for Disease Control (China CDC) and colleagues, posted on Research Square in February 2022. Researchers have asked for that data to be made public on several occasions, without success.<\/p>\n\n\n\n

But Florence D\u00e9barre, an evolutionary biologist at the French National Centre for Scientific Research, who is also a co-author on the latest report, discovered the data almost by chance on the public data repository GISAID on 4 March. \u201cBasically, [they\u2019re] the ones we\u2019ve been waiting for, for a year,\u201d she says.<\/p>\n\n\n\n

In total, D\u00e9barre and her colleagues downloaded around half a terabyte of genomic data from some 50 samples. The data included almost all the swabs taken from drains, market stalls and the ground between January and February 2020 that had tested positive for SARS-CoV-2. \u201cWe\u2019re talking about millions and millions of sequencing reads,\u201d says Crits-Christoph.<\/p>\n\n\n\n

But soon after the researchers downloaded the data, it disappeared from public view on GISAID.<\/p>\n\n\n\n

A spokesperson for GISAID told Nature<\/em> in an e-mail that it does not delete records, but that contributors often update their records, and, during that time, records \u201cbecome temporarily invisible\u201d. The market-swab data \u201care currently being updated with newer and additional data as part of a manuscript currently under review\u201d. (The Gao paper is marked as \u2018under review\u2019 at Nature Portfolio Nature<\/em>\u2019s news team is independent of its publisher Springer Nature, which publishes Nature Portfolio.)<\/p>\n\n\n\n

D\u00e9barre and her colleagues say they reached out to authors of the preprint to collaborate on the analysis, but the China CDC declined. On 14 March, her colleagues, as well as members of the China CDC, presented their work to the WHO at a meeting of the Scientific Advisory Group for the Origins of Novel Pathogens, a body tasked with investigating outbreaks, including the origins of SARS-CoV-2.<\/p>\n\n\n\n

At the WHO press briefing on 17 March, Tedros called on the China CDC researchers to be transparent in sharing data. \u201cThese data could have and should have been shared three years ago,\u201d he said.<\/p>\n\n\n\n

Gao did not respond to Nature<\/em>\u2019s requests for comment.<\/p>\n\n\n\n

D\u00e9barre recognizes that it has taken a long time to share this data, but acknowledges the environmental sampling and sequencing work conducted by the China CDC. \u201cThey did what needed to be done,\u201d she says. \u201cWe wouldn\u2019t have this data, if it wasn\u2019t for their work.\u201d<\/p>\n\n\n\n

Wild match<\/strong><\/h2>\n\n\n\n

Previous studies have found that Chinese bamboo rats (Rhizomys sinensis<\/em>) and raccoon dogs were sold at the Huanan market between May 2017 and November 20193<\/a><\/sup>, and that several stalls were probably selling live or freshly killed mammals or other meat products4<\/a><\/sup>. The data confirm that \u201cexactly what we thought was there in the market, was there in the market\u201d, says Joel Wertheim, a molecular epidemiologist at the University of California, San Diego, and another co-author of the analysis.<\/p>\n\n\n\n

The area where most of the SARS-CoV-2-positive samples clustered was also where most of the samples containing wild-animal DNA were found, which Poon says \u201cagrees with the hypothesis that maybe the virus came from animals\u201d. Positive swabs from the eastern section of the market primarily contained human DNA \u2014 suggesting that there was some human-to-human transmission at the market in early 2020, says Poon.<\/p>\n\n\n\n

In one sample from a cart used to move cages, the researchers found RNA and DNA that matched the raccoon-dog genome, and very little that matched the human genome. \u201cThe most logical hypothesis is that raccoon dogs were infected by SARS-CoV-2 and shed the virus,\u201d says Poon.<\/p>\n\n\n\n

But it is possible that the site was contaminated with SARS-CoV-2 RNA from other sources. \u201cThere is no evidence that the virus came from an infected raccoon dog; it could just as easily have come from an infected person,\u201d says Kinney.<\/p>\n\n\n\n

More data<\/strong><\/h2>\n\n\n\n

Many more forensic insights could still come from the data if they were made public again, says Crits-Christoph. For example, by looking at the ratio of RNA to DNA for different animal species, researchers could determine how recently those animals were present at the market, because DNA typically persists in the environment longer than RNA does. But more details are needed about how the samples were collected, processed and sequenced, says Wertheim.<\/p>\n\n\n\n

A close study of the RNA data could possibly determine whether the animals at the market were sick, adds Crits-Christoph. Does it seem like the creatures were in \u201ca disease state, or a healthy state?\u201d he asks. \u201cThere\u2019s all sorts of wonderful, complex questions in the data.\u201d<\/p>\n\n\n\n

There are more data that have not yet been shared \u2014 including environmental swabs that were negative for SARS-CoV-2, and detailed virus data. Those data are important to analyse, to get a better picture of what was happening at the market, says Wertheim.<\/p>\n<\/div><\/div>","protected":false},"excerpt":{"rendered":"

Nature Some scientists say the analysis provides new evidence supporting the hypothesis that the virus that causes COVID-19 spilled over from an animal \u2014 but falls short of definitive proof. Raccoon dogs, bamboo rats, palm civets: these are just some of the animals whose DNA has been found in swabs taken from the Huanan Seafood […]<\/p>\n","protected":false},"author":11,"featured_media":2928,"comment_status":"open","ping_status":"closed","sticky":false,"template":"","format":"standard","meta":{"_jetpack_memberships_contains_paid_content":false,"footnotes":"","jetpack_publicize_message":"@Nature article on the origins of #COVID @GISAID removes data from public view","jetpack_publicize_feature_enabled":true,"jetpack_social_post_already_shared":false,"jetpack_social_options":{"image_generator_settings":{"template":"highway","default_image_id":0,"font":"","enabled":false},"version":2}},"categories":[37,7,21],"tags":[],"class_list":["post-2927","post","type-post","status-publish","format-standard","has-post-thumbnail","hentry","category-avian-influenza","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-2023-03-21-at-21.49.21.png","jetpack_sharing_enabled":true,"_links":{"self":[{"href":"https:\/\/www.unmc.edu\/healthsecurity\/transmission\/wp-json\/wp\/v2\/posts\/2927","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=2927"}],"version-history":[{"count":1,"href":"https:\/\/www.unmc.edu\/healthsecurity\/transmission\/wp-json\/wp\/v2\/posts\/2927\/revisions"}],"predecessor-version":[{"id":2929,"href":"https:\/\/www.unmc.edu\/healthsecurity\/transmission\/wp-json\/wp\/v2\/posts\/2927\/revisions\/2929"}],"wp:featuredmedia":[{"embeddable":true,"href":"https:\/\/www.unmc.edu\/healthsecurity\/transmission\/wp-json\/wp\/v2\/media\/2928"}],"wp:attachment":[{"href":"https:\/\/www.unmc.edu\/healthsecurity\/transmission\/wp-json\/wp\/v2\/media?parent=2927"}],"wp:term":[{"taxonomy":"category","embeddable":true,"href":"https:\/\/www.unmc.edu\/healthsecurity\/transmission\/wp-json\/wp\/v2\/categories?post=2927"},{"taxonomy":"post_tag","embeddable":true,"href":"https:\/\/www.unmc.edu\/healthsecurity\/transmission\/wp-json\/wp\/v2\/tags?post=2927"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}