The study utilized samples collected by Chinese officials in the early stages of the coronavirus outbreak, which are considered one of the most valuable scientific sources of information regarding the origins of the pandemic. The samples were collected in January 2020 in the city of Wuhan, China.
The early connection was made between the mysterious pneumonia cases presenting at hospitals in Wuhan and the Huanan Seafood Wholesale Market. After the market was closed, authorities collected swab samples from various locations, including stalls, the insides of animal cages, and equipment used for skinning slaughtered animals.
The analyses of these samples were published last year, and the raw data was made available for other scientists to use.
Now, a group of scientists in the United States and France reports that more advanced genetic analyses have allowed them to examine the early days of the coronavirus in greater depth. As part of this study, they needed to analyze millions of short genetic code fragments (both DNA and RNA) to effectively "reconstruct" the animals and viruses that were present in the market in January 2020.
Professor Florence Débarre from the French National Center for Scientific Research stated, "With the environmental samples, we see the DNA and RNA remnants of these animals, and some of them were on the stalls where [the COVID virus] was found." The research results published in the journal Cell present findings that support the theory that the virus emerged in the market.
According to this, it was determined that the coronavirus and the animals susceptible to transmission were present in the same location; in some swabs, both the animal's and the coronavirus's genetic code were observed together. These findings were not evenly distributed throughout the market but were concentrated in specific hotspots.
Professor Kristian Andersen from the Scripps Research Institute stated, "Even at the level of a single stall, we find a very consistent story indicating that the likely source of the outbreak is the market." However, the mere presence of the virus and the animals at the same time and place does not prove that the animals were infected.
The most commonly identified animal in the samples was the raccoon dog. Experiments have shown that this animal can both catch and transmit COVID. Other animals identified as potential sources of the pandemic include the masked palm civet, which was also linked to the SARS outbreak in 2003, as well as the white-bellied rat and Malayan porcupines. However, no experiments were conducted to determine whether these animals could spread the virus.
The depth of the genetic analysis allowed researchers to identify which species of raccoon dogs were being sold in the market. These species are more commonly found in the wild in southern China, providing scientists with clues about where to look next in their investigations.
The research team also compared the genetic code of the viral samples found in the market with samples taken from patients in the early days of the pandemic. Examining the various mutations in the viral samples provided additional clues. The samples suggest that the coronavirus emerged multiple times in the market and that two potential transmission events from animals to humans occurred, but this does not provide definitive proof.
Researchers state that this supports the idea that the market was the origin of the outbreak rather than the virus starting elsewhere and then gaining strength in the market. Scientists also used the mutations to construct the virus's family tree and to trace its history.
Professor Andersen stated, "The times we believe the pandemic and the outbreak in the market began overlap; they are the same." According to their research, all the genetic diversity of the coronavirus observed in the early days of the pandemic was present in the market.
Professor Michael Worobey from the University of Arizona stated, "Rather than being a small branch on this large, complex evolutionary tree, the genetic sequences from the market are spread across all branches, which is consistent with the idea that genetic diversity actually began in the market." He added that when this study is combined with other data, such as early cases and hospitalizations linked to the market, it indicates that the origins of the coronavirus are animal-based.
Professor Worobey stated, "This has emerged in a way that leaves no room for doubt," and noted that, given the data, alternative explanations require "rather fanciful, absurd scenarios." He added, "I think there has been a lack of appreciation for how strong the evidence is thus far."
The lab leak theory posits that the coronavirus originated from the Wuhan Institute of Virology (WIV), which has been studying coronaviruses for a long time. This facility is located about a 40-minute drive from the market. U.S. intelligence agencies had been asked to investigate whether the leak was accidental or intentional.
In June 2023, all agencies involved in the process stated that both the leak and animal origin scenarios remained plausible for the outbreak. The National Intelligence Council and four other agencies indicated that the potential source was likely animals. Meanwhile, the Federal Bureau of Investigation (FBI) and the Department of Energy argued that the likelihood of a laboratory origin was higher.
Professor Andersen stated, "For many who think, 'The lab is nearby, it must be the lab,' this seems like the most likely scenario. I understand that argument." However, he emphasizes that there is now a substantial amount of data indicating that the market is the "real epicenter" and that it even points to "specific locations within that market."
Identifying the animals that could be the source of the pandemic provides scientists with clues about where to search for more evidence regarding this origin. However, since farms culled their animals during the early days of the coronavirus, there may no longer be evidence to be found. Professor Worobey stated, "We likely missed our chance."
Professor Alice Hughes from the University of Hong Kong, who was not involved in the analysis, described the research as "a good study." However, she added, "We cannot achieve a higher level of certainty without swab samples taken from the actual animals in the market." Professor James Wood, Co-Director of the Cambridge Infectious Diseases Institute, stated that the study provides "very strong evidence" that the outbreak began with wildlife at the stalls in the market.
However, he noted that since the samples were collected after the market was closed and the outbreak likely began weeks earlier, the findings cannot be definitive. Professor Wood warned that "almost nothing has been done" to restrict the live wildlife trade. He added that the uncontrolled transmission of viruses from infected animals poses a significant risk for future outbreaks.
