Chinese scientists have published their long-awaited genetic analysis of the samples and smears they collected in early 2020 at the Huanan Seafood Market, the first epicenter of the pandemic.
In the study, published Wednesday in Nature, the authors acknowledge for the first time that wild animals susceptible to SARS-CoV-2 infection — including raccoon dogs — were present on the market amid the abundance of genetic traces of SARS. -CoV-2 and humans. . But the overall analysis is flawed, pointing to the presence of animals that were almost certainly off the market, including giant pandas, chimpanzees and Atlantic gray seals. The authors continued to downplay the potential that a virus spillover from wildlife to humans in the crowded marketplace was the spark that ignited the pandemic. Instead, they repeatedly advanced, without evidence, hypotheses favored by Chinese officials, namely that the virus was marketed via humans or frozen foods, and that the bustling location became an amplifier site for infection.
Still, the publication of the data is important – and it will be for a long time. Although the samples were collected from January 1 to March 30, 2020, a draft of the study and some of the data was not first released in a preprint until 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 common among people in the marketplace before it closed on the morning of Jan. 1. The authors, led by scientists from China’s Centers for Disease Control and Prevention (China CDC), noted that they had also tested some of the animals on 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 publication in Nature, Chinese CDC scientists quietly uploaded previously undisclosed metagenomic data from the samples to 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 China’s CDC scientists about a possible collaboration. The Chinese CDC scientists responded by having their data removed from public view, and GISAID publicly accused the international researchers of violating the terms of service, which they have emphatically denied.
However, amid the data access dispute, the international group published a preliminary analysis of the data, without publishing the underlying genetic data themselves to avoid “bragging” their Chinese colleagues. Overall, that preliminary analysis showed that the environmental samples from the market were not only positive for SARS-CoV-2 and human genetics — as the 2022 preprint suggested — but were also chock-full of genetic traces from 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 theorist specializing 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 in the marketplace.
The analysis cannot determine whether the animals were infected with the pandemic virus or, if so, whether there was animal-to-human or human-to-animal transmission. So it cannot definitively determine how the pandemic started. However, as many virologists and infectious disease experts have since pointed out, this close mixing of genetics in a suspect market at the epicenter of early cases, if a natural spillover event were to trigger the pandemic, is exactly the kind of genetic evidence that scientists would expect. find afterwards. Such markets, with a menagerie of wildlife in close, crowded conditions with humans, are known to act as hotbeds of viral adaptation risk and spillover effects.
Worobey and his colleagues focused in particular on one sample from a cart — Q61 or env_0576 — which was surrounded by a high density of SARS-CoV-2-positive samples and itself teeming with genetic material from raccoon dogs. 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 points to the possibility that the SARS-CoV-2 present came from the raccoon dog and not humans.
