Update (20 March): The analysis by Florence Débarre and colleagues of the China market data she uncovered has now been posted online.

The origin of COVID-19 has been a fundamental question: Was it from nature or a lab? In this post, I’ll be able to shed light on this question. A few days ago, Florence Debarre, a French evolutionary biologist, identified previously undisclosed genetic data from the Wuhan Seafood Market. She shared her findings with Kristen Andersen. Andersen is an evolutionary biologist at Scripps Research who co-published one of the first research papers on the origin of COVID-19 in 2020. Together they believe these new findings support a natural source of the virus rather than from a lab.

The most likely location of the origin of COVID-19 is in Wuhan, the largest city in Central China with a population greater than 11 million. But, it most likely was not the result of a lab accident at the Wuhan Institute of Virology. Even though The FBI and the United States Department of Energy said the origin of COVID-19 was a lab leak, they said so with low confidence. The truth is they did not base their view on scientific research evidence. It was subjective and based on assumptions with little or no data. Unfortunately, their pronouncements had the effect of swaying Americans’ opinions about the origin of the virus. Most Americans believe Covid emerged from a Chinese Bio-Lab.

Wuhan Huanan Seafood Market

In The Trump Files, I discussed the origins of COVID-19 and reviewed some of the research published between 2020 – 2022 on COVID-19’s source. I reported then that the most likely place that the spillover happened was the Wuhan Huanan Seafood Wholesale Market. A third of the 168 COVID-19 cases were linked to the market. It was also discovered that many early cases were related to the market and the western market where live animals, such as raccoon dogs, were housed. Raccoon dogs are potential intermediate hosts to transmit SARS-CoV-2 to humans.

Chinese researchers, who sampled most stalls at the market posted their results on GISAID (Global Initiative on Sharing Avian Influenza Data), a virology database from January – March 2020.

The Pandemic’s Origin

Katherine J. Wu, in an article in The Atlantic, reports that the most substantial evidence yet that an animal started the pandemic was after samples from raccoon dogs showed the genetic markers of COVID-19. However, you are going to find out that the finding was unexpected.

There are two competing ideas to explain the origin of the virus. One is a natural spillover event from animal to human. The other is a speculative notion that the pandemic originated in the Wuhan Institute of Virology from some lab leak or accidental release. As Wu points out, the lab leak emerged because of China’s reluctance to share information and politicization by the United States.

The Lab Leak Idea

The Trump administration pushed the lab leak theory in the press to take the heat of their own bungling in dealing with the spread of the virus in the United States. No evidence existed then for a lab leak, and it is more unlikely now based on recent research reported in peer-reviewed journals and newsletters.

The major perpetrator of the lab leak theory is the media; it makes for good television. It also enables the media to present two sides of the origin of COVID-19, which is very similar to the media’s enchantment of presenting two sides of other issues, such as evolution versus intelligent design. In a Los Angeles Times article, Michael Hitzik describes how CNN propped up the lab leak idea by bringing together a group of four panelists, only one of whom was a medical expert—Sanjay Gupta. The lab leak side had no one with any experience in virology. The two ideas, a natural spillover and the lab leak, as equals is the unfortunate approach the media takes. There are many research studies in scientific journals about the origin of COVID-19 that support a natural spillover from animal to human. There are no studies that support a lab leak.

Spillover Infection Events

Pathogens such as SARS-CoV-2 are the result of spillover infection events. Spillover occurs when a reservoir population (rats, bats, mosquitos) encounters a novel host population, such as humans. This is an example of zoonosis, an infectious disease caused by an agent such as a bacterium, parasite, or virus that has spilled over or jumped from an animal (normally a vertebrate) to a human. According to many scientists around the world, a spillover occurred somewhere in China from a bat to an intermediate animal and then to a human. A SARS-CoV-2 infection can spread from human to human. The infection can spread asymptomatically.

Dr. Anthony Fauci, former director of the NIAID, says 40 percent of Americans with SARS-CoV-2 are asymptomatic, meaning they show no disease symptoms. According to the CDC, people can be infectious for ten to fourteen days. South Korean researchers estimate those transferable symptoms were contagious for up to twenty days. The most likely place that the spillover happened was the Huanan market. It’s been reported that a third of the 168 COVID-19 cases reported in December 2019 were linked to the market. It was also discovered that many of the early cases were related to the market and the western part of the market where live animals, such as raccoon dogs, were housed. Raccoon dogs are potential intermediate hosts to transmit SARS-CoV-2 to humans.

Unearthing Evidence from Samples Collected at the Huanan Seafood Market

An international team of virologists, genomicists, and evolutionary biologists have found that raccoon dogs, sold illegally at the market, may have been carrying and perhaps shedding the virus as early as the end of 2019. Florence Débarre, a theoretician specializing in evolutional biology and working at CNRS, the French national research agency, unearthed the data. The data consist of genetic sequences posted on GISAID (Global Initiative on Sharing Avian Influenza Data), a virology database, by Chinese researchers.

Data on SARS-CoV-2 from China, Jan. 10, 2020

It’s important to note that on January 10, 2020, critical public health responses around the globe were kicked off, when China CDC shared via GISAID the first SARS-CoV-2 whole-genomes and associated data. According to GISAID this curated, high-quality data made available through GISAID permitted the initiation of the development of the first vaccines, diagnostic tests, and other responses at unprecedented speed, including the first vaccines to be approved and made available (Polack et al N Engl J Med 2020), and development of the first NAAT and RT-PCR-based molecular tests to detect the pandemic coronavirus (Bohn et al Clin Chem Lab Med 2020).

An award-winning science journalist, Michael Le Page, wrote in an article in NewScientist that analyses of the earliest covid-19 cases had strengthened the argument that the coronavirus pandemic began when animals at the Wuhan Seafood Market passed the virus on to people. He stated that the first case involved a woman working as a market vendor. She became ill on December 11, 2019.

Early Research Papers on Origins of COVID-19—the Anderson Study.

One of the first papers on the origin of SARS-CoV-2 was reported by Dr. Francis Collins, director of the NIH, on the director’s blog. The research Dr. Collins cites, “The Proximal Origin of SARS-CoV-2,” shows that the virus arose naturally, not in a lab. It was published in Nature Medicine, a journal in the Nature publishing portfolio. The paper was also cited in Rasmussen’s “On the Origins of SARS-CoV-2” research and also counters the laboratory origin theory of SARS-CoV-2. One scenario postulated by the research team was natural selection in an animal host before zoonotic transfer. Given the similarity of SARS-CoV-2 to SARS-CoV-like coronaviruses in bats, the researchers suggest that bats likely serve as reservoir hosts for their progenitor.

They also suggest natural selection in an animal host before zoonotic transfer. Given the similarity of SARS-CoV-2 to SARS-CoV-like coronaviruses in bats, the researchers suggest it is likely that bats serve as reservoir hosts for their progenitor.

Florence Débarre’s COVID-19 Findings

An international team of virologists, genomicists, and evolutionary biologists have found that raccoon dogs, sold illegally at the Wuhan Seafood Market, may have been carrying and perhaps shedding the virus as early as the end of 2019. Florence Débarre, a theoretician specializing in evolutional biology and working at CNRS, the French national research agency, unearthed the data. The data consist of genetic sequences posted by Chinese researchers on GISAID (Global Initiative on Sharing Avian Influenza Data), a virology database. Since Débarre identified the lines, the Chinese removed them (which is permissible because they submitted them).

Débarre’s findings were presented on March 12, 2023, to the Scientific Advisory Group for the Origins of Novel Pathogens (SAGO). This is a link to SAGO’s statement based on Débarre’s presentation. Here are some key statements from SAGO about this new data that sheds light on the origin of Covid.

Awareness of Débarre’s Work

On 12 March 2023, WHO was made aware of new SARS-CoV-2 sequences and metagenomics data associated with samples collected in the Huanan Seafood Wholesale Market, Wuhan, China, from January 2020, that became available on GISAID for a short period. The data had subsequently been downloaded by a number of researchers from several countries. Access was restricted shortly after, apparently to allow further data updates by China CDC.  WHO then immediately reached out to China CDC and to the Chair and Vice-Chair of SAGO. Upon discussions between WHO and Chinese colleagues, it was explained that the genomic data are the basis for an expected update to the existing Liu et al. 2022 preprint (1), which is in the process of being re-submitted for publication to Nature by China CDC.

SAGO initial statement revealing the key discovery by Florence Débarre.

After discussions with the WHO secretariat and the SAGO Chair and Vice-Chair, a call was arranged on 12 March with the scientists involved from China CDC, and some of those who had accessed the data from GISAID, to gauge the significance of this data and the analyses of this data. WHO subsequently organized a meeting on 14 March 2023 with all SAGO members, and invited researchers from China CDC to present the updated analysis of their data. WHO and SAGO also invited the researchers who had informed WHO that they had accessed data from GISAID, to present their analysis of the temporarily released sequences. 

The presentations from China CDC and invited international researchers indicated that there were newly available data from the Huanan Seafood Wholesale Market. This included metagenomic data of environmental samples from various stalls and wastewater collection sites collected as early as January 2020. Analyses of these data suggest that apart from SARS-CoV-2 sequences, some samples also contained human DNA, as well as mitochondrial DNA of several animal species, including some that are known to be susceptible to SARS-CoV-2. This included DNA from wild raccoon dogs, Malaysian porcupine, and bamboo rats among others, in SARS-CoV-2 positive environmental samples.

Conclusion

The findings suggest that animals were present at the market shortly before the market had been cleared on 1 January 2020, as part of the public health measures by Chinese authorities. These results provide potential leads to identifying intermediate hosts of SARS-CoV-2 and potential sources of human infections in the market.

SAGO’s interpretation of Débarre’s discorvery.

The SAGO report, quoted here, is preliminary and does not settle the case of a natural origin vs. a lab origin; it leads us in a direction based on observations, sampling, and data analysis. We don’t have any data like this to support a lab origin. But it still needs to rule out a lab origin. It’s on the table but occupies only a sliver.

References

Andersen, K.G., Rambaut, A., Lipkin, W.I. et al. The proximal origin of SARS-CoV-2. Nat Med 26, 450–452 (2020).

Cohen, Jon. Unearthed genetic sequences from China market may point to animal origin of COVID-19. Science insider, March 16, 2023.

Hassard, Jack. The Trump Files: An Account of the Trump Administration’s Effect on American Democracy, Human Rights, Science and Public Health (p. 318). Northington-Hearn Publishing LLC. Kindle Edition.

SAGO statement on newly released SARS-CoV-2 metagenomics data from China CDC on GISAID, March 18, 2023.

Wu, Katherine J. The Strongest Evidence Yet That an Animal Started the Pandemic. The Atlantic, March 16, 2023