Chinese scientists have published their long-awaited genetic analysis of the samples and swabs they collected in early 2020 from the Huanan Seafood Market, the initial epicenter of the pandemic.

In the study, published Wednesday in Nature, the authors acknowledge for the first time that wildlife susceptible to SARS-CoV-2 infection—including raccoon dogs—were present in the market amid the plethora of genetic traces from SARS-CoV-2 and humans. But, the overall analysis is flawed, indicating the presence of animals that were almost certainly not at the market, including giant pandas, chimpanzees, and Atlantic grey seals. The authors continued to downplay the potential that a virus spillover from wildlife to humans in the crowded market was the spark that ignited the pandemic. Instead, they repeatedly put forward, without evidence, hypotheses favored by Chinese officials, namely that the virus was carried into the market via humans or frozen foods, and the bustling venue became an amplifier site for infection.

Still, the publication of the data is momentous—and a long time coming. Though the samples were collected from January 1 to March 30 of 2020, a draft of the study and some of the data were only first released in a preprint two years later, in February 2022. The preprint reported that SARS-CoV-2 was abundant amid human genetic material from the samples, indicating that the virus was prevalent among people at the market before it was shuttered on the morning of January 1. The authors, led by scientists at China's Centers for Disease Control and Prevention (China CDC), noted that they had also tested some animals in the market—mostly rabbits, stray cats, and snakes—but all were negative for SARS-CoV-2.

Withheld data

It wasn't until last month, three years after the samples were collected, that more genetic information from those samples came to light. In preparation for the publication in Nature, China CDC scientists quietly uploaded previously undisclosed metagenomic data from the samples onto a public genetic database, called GISAID, sometime in January. In early March, a group of independent international scientists noticed the data, eagerly downloaded it, and began analyzing it while reaching out to the China CDC scientists about a possible collaboration. The China CDC scientists responded by having their data pulled from public view, and GISAID publicly accused the international researchers of breaching terms of service, which they have emphatically denied.

Amid the data-access dispute, however, the international group published a preliminary analysis of the data, without publishing the underlying genetic data itself to avoid "scooping" their Chinese colleagues. Overall, that preliminary analysis showed that the environmental samples from the market were not just positive for SARS-CoV-2 and human genetic material—as the 2022 preprint suggested—but were also brimming with genetic traces of wildlife, including some known to be susceptible to SARS-CoV-2 infections, such as raccoon dogs.

The study—led by Michael Worobey, an evolutionary biologist at the University of Arizona; Kristian Andersen, a virologist at the Scripps Research Institute in California; and Florence Débarre, a theoretician who specializes in evolutionary biology at France's national research agency, CNRS—provided the first genetic evidence linking SARS-CoV-2-positive samples, humans, and susceptible wild animals together in the market.

The analysis cannot determine if the animals were infected with the pandemic virus, or, if they were, whether any animal-to-human or human-to-animal transmission occurred. Thus, it can't conclusively determine how the pandemic began. However, as many virologists and infectious disease experts have since noted, if a natural spillover event did spark the pandemic, this close mingling of genetic material in a suspect market at the epicenter of early cases is exactly the type of genetic evidence scientists would expect to find after the fact. Such markets, with a menagerie of wildlife in close, crowded conditions with humans, are known to act as hotbeds of risk for viral adaption and spillovers.

In particular, Worobey and his colleagues focused on one sample from a cart—Q61 or env_0576—that was surrounded by a high-density of SARS-CoV-2 positive samples and was, itself, teeming with raccoon dog genetic material. The researchers found that the sample contained 1,252 genetic fragments with 100 percent identity to the raccoon dog genome with no such perfect matches to the human genome. The finding hints at the possibility that the SARS-CoV-2 present was from the raccoon dog, not humans.