Inquiries into the origins of SARS-CoV-2
Since the beginning of the COVID-19 pandemic, there have been efforts by scientists, governments, and others to determine the origin of the SARS-CoV-2 virus. Similar to other outbreaks, the virus was derived from a bat-borne virus and most likely was transmitted to humans via another animal in nature, or during wildlife bushmeat trade such as that in food markets. While other explanations, such as speculations that SARS-CoV-2 was accidentally released from a laboratory have been proposed, such explanations are not supported by evidence. Conspiracy theories about the virus's origin have also proliferated.
Research is ongoing as to whether SARS-CoV-2 came directly from bats or indirectly through an intermediate host, such as pangolins, civets, or raccoon dogs. Genomic sequence evidence indicates the spillover event introducing SARS-CoV-2 to humans likely occurred in late 2019. As with the 2002–2004 SARS-CoV-1 outbreak, efforts to trace the specific geographic and taxonomic origins of SARS-CoV-2 could take years, and results may be inconclusive.
In July 2022, two papers published in "Science" described novel epidemiological and genetic evidence that suggested the pandemic likely began at the Huanan Seafood Wholesale Market and did not come from a laboratory.
Zoonosis.
While there are multiple proposed explanations for how SARS-CoV-2 was introduced into and evolved adaptations suited to human populations, there is significant evidence and agreement that the most likely original viral reservoir for SARS-CoV-2 is horseshoe bats. The closest known viral relatives of SARS-CoV-2 are RaTG13 and BANAL-52, sampled from horseshoe bat droppings in Yunnan province in China and Feuang, Laos, respectively. The evolutionary distance between SARS-CoV-2 and RaTG13 is estimated to be about 50 years (between 38 and 72 years).
Bats are a significant reservoir species for a diverse range of coronaviruses, and humans have been found with antibodies for them suggesting that direct infection by bats is common. The zoonotic transmission of SARS-CoV-2 virus to humans took place in the context of exacerbating factors that could make such spillovers more likely. Human contact with bats has increased as human population centers encroach on bat habitats. Several social and environmental factors including climate change, natural ecosystem destruction and wildlife trade have also increased the likelihood for the emergences of zoonosis. One study made with the support of the European Union found climate change increased the likelihood of the pandemic by influencing distribution of bat species.
The earliest human cases of SARS-CoV-2 were identified in Wuhan, but the index case remains unknown. RaTG13 was sampled from bats in a mine in Mojiang County, Yunnan, located roughly away from Wuhan, and there are relatively few bat coronaviruses from Hubei province, where Wuhan is located.
Intermediate host.
In addition to direct spillover, another pathway, considered highly likely by scientists, is that of transmission through an intermediate host. Specifically, this implies that a cross species transmission occurred prior to the human outbreak and that it had pathogenic results on the animal. This pathway has the potential to allow for greater adaptation to human transmission via animals with more similar protein shapes to humans, though this is not required for the scenario to occur. The evolutionary separation from bat viruses is explained in this case by the virus's presence in an unknown species with less viral surveillance than bats. The virus's ability to easily infect and adapt to additional species (including mink) provides evidence that such a route of transmission is possible.
A 2024 study of samples collected from Huanan Seafood Wholesale Market found genetic material of various possible intermediate hosts. The most likely were raccoon dogs. Additionally, the study suggests the raccoon dogs may have come from southern China, where the closest-known relatives to SARS-CoV-2 were found in bats.
Unlikely scenarios.
While the scientific consensus is that SARS-CoV-2 derived from viruses hosted in bats, the precise means by which this occurred has been sometimes subject to speculation. Below are some scenarios judged to be unlikely.
Cold food chain.
Another proposed introduction to humans is through fresh or frozen food products, referred to as the cold food chain. Scientists do not consider this to be a likely origin of SARS-CoV-2 in humans. This scenario's source animal could be either a direct or intermediary species as described above. Many investigations centered around the Huanan Seafood Wholesale Market in Wuhan, which had an early cluster of cases. While there have been food-borne outbreaks of human viruses in the past, and evidence of re-introduction of SARS-CoV-2 into China through imported frozen foods, investigations found no conclusive evidence of viral contamination in products at the Huanan Market.
Investigations.
Chinese government.
The first investigation conducted in China was by the Wuhan Municipal Health Commission, responding to hospitals reporting cases of pneumonia of unknown etiology, resulting in the closure of the Huanan Seafood Wholesale Market on 1 January 2020 for sanitation and disinfection. The Chinese Center for Disease Control and Prevention (CCDC) entered the market the same day and took samples; as the animals had been removed before public-health authorities came in, no animals were sampled, although that would have been more conclusive.
In April 2020, China imposed restrictions on publishing academic research on the novel coronavirus. Investigations into the origin of the virus would receive extra scrutiny and must be approved by Central Government officials. The restrictions do not ban research or publication, including with non-Chinese researchers; Ian Lipkin, a US scientist, has been working with a team of Chinese researchers under the auspices of the Chinese Center for Disease Control and Prevention, a Chinese government agency, to investigate the origin of the virus. Lipkin has long-standing relationships with Chinese officials, including premier Li Keqiang, because of his contributions to rapid testing for SARS in 2003.
The Huanan live-animal market was suspected of being the source of the virus, as there was a major, early cluster of cases there. On 31 January 2021, a team of scientists led by the World Health Organization visited the market to investigate the origins of COVID-19. Based on the existing evidence, the WHO concluded that the origin of the virus was still unknown, and the Chinese government insisted that the market was not the origin. The Chinese government has long insisted that the virus originated outside China, and until June 2021 denied that live animals were traded at the Huanan market.
Some Chinese researchers had published a preprint analysis of the Huanan swab samples in February 2022, concluding that the coronavirus in the samples had likely been brought in by humans, not the animals on sale, but omissions in the analysis had raised questions, and the raw sample data had not yet been released.
On March 4, 2023, the data from the swab samples of the Huanan live-animal market were released, or possibly leaked; a preliminary analysis of this data was reviewed by the international research community, which said that it made an animal origin much more likely. Although the samples do not definitively prove that the raccoon dog is the "missing" intermediate animal host in the bat-to-human transmission chain, it does show that common raccoon dogs were present in the Huanan market at the time of the initial SARS-CoV-2 outbreak, in areas that were also positive for SARS-CoV-2 RNA, and substantially strengthens this hypothesis as the proximal origin of the pandemic.
An attempt by these researchers to collaborate with the Chinese researchers was not answered, but the raw data was removed from the online database. On March 14, an international group of researchers presented a preliminary analysis at a meeting of the World Health Organization's Scientific Advisory Group for Origins of Novel Pathogens, at which Chinese COVID-19 researchers were also present. On the sixteenth, George Gao, the former head of the CCDC and lead author on the February 2022 preprint, told "Science" that there was "nothing new" in the raw data, and refused to answer questions about why his research team had removed it from the database.
On March 17, the WHO director-general said that the data should have been shared three years earlier, and called on China to be more transparent in its data-sharing. There exists further data from further samples which has not yet been made public. Maria Van Kerkhove, the WHO's COVID-19 technical lead, called for it to be made public immediately (see Huanan live-animal market#Swabs).
United States government.
Trump administration.
On 6 February 2020, the director of the White House's Office of Science and Technology Policy requested the National Academies of Sciences, Engineering, and Medicine to convene a meeting of "experts, world class geneticists, coronavirus experts, and evolutionary biologists", to "assess what data, information and samples are needed to address the unknowns, in order to understand the evolutionary origins of COVID-19 and more effectively respond to both the outbreak and any resulting information".
In April 2020, it was reported that the US intelligence community was investigating whether the virus came from an accidental leak from a Chinese lab. The hypothesis was one of several possibilities being pursued by the investigators. US Secretary of Defense Mark Esper said the results of the investigation were "inconclusive". By the end of April 2020, the Office of the Director of National Intelligence said the US intelligence community believed the coronavirus was not man-made or genetically modified.
US officials criticised the "terms of reference" allowing Chinese scientists to do the first phase of preliminary research. On 15 January 2021, US Secretary of State Mike Pompeo said that to assist the WHO investigative team's work and ensure a transparent, thorough investigation of COVID-19's origin, the US was sharing new information and urging the WHO to press the Chinese government to address three specific issues, including the illnesses of several researchers inside the WIV in autumn 2019 "with symptoms consistent with both COVID-19 and common seasonal illnesses", the WIV's research on "RaTG13" and "gain of function", and the WIV's links to the People's Liberation Army. On 18 January, the US called on China to allow the WHO's expert team to interview "care givers, former patients and lab workers" in the city of Wuhan, drawing a rebuke from the Chinese government. Australia also called for the WHO team to have access to "relevant data, information and key locations".
A classified report from May 2020 by the Lawrence Livermore National Laboratory, a US government national laboratory, concluded that the hypothesis that the virus leaked from the WIV "is plausible and deserves further investigation", although the report also notes that the virus could have developed naturally, echoing the consensus of the American intelligence community, and provides no "smoking gun" towards either hypothesis.
Biden administration.
On 13 February 2021, the White House said it had "deep concerns" about both the way the WHO's findings were communicated and the process used to reach them. Mirroring concerns raised by the Trump administration, National Security Adviser Jake Sullivan stated that it was essential that the WHO-convened report be independent and "free from alteration by the Chinese government". On 14 April 2021, the Director of National Intelligence Avril Haines, along with other Biden administration officials, said that they had not ruled out the possibility of a laboratory accident as the origin of the COVID-19 virus.
On 26 May 2021, President Joe Biden directed the U.S. intelligence community to produce a report within 90 days on whether the COVID-19 virus originated from human contact with an infected animal or from an accidental lab leak, stating his national security staff said there is insufficient evidence to determine either hypothesis to be more likely. On 26 August 2021, the Office of the Director of National Intelligence released an unclassified summary of their findings, with the main point being that the report remained inconclusive as to the origin of the virus, with intelligence agencies divided on the question. The report also concluded that the virus was most likely not genetically engineered, and that China had no foreknowledge of the virus prior to the outbreak. The report concluded that a final determination of the origin was unlikely without cooperation from the Chinese government, saying their prior lack of transparency "reflect[ed] in part China's government's own uncertainty about where an investigation could lead, as well as its frustration that the international community is using the issue to exert political pressure on China." Chinese foreign ministry spokesman Wang Wenbin said that the US intelligence report was "unscientific and has no credibility".
On 23 May 2021, "The Wall Street Journal" reported that a previously undisclosed US intelligence report stated that three researchers from the Wuhan Institute of Virology became ill enough in November 2019 to