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Scientists have released three studies that reveal intriguing new clues about how the COVID-19 pandemic started. Two of the reports trace the outbreak back to a massive market that sold live animals, among other goods, in Wuhan, China1,2, and a third suggests that the coronavirus SARS-CoV-2 spilled over from animals — possibly those sold at the market — to humans at least twice in November or December 20193. Posted on 25 and 26 February, all three are preprints, and so have not been published in a peer-reviewed journal.

These analyses add weight to original suspicions that the pandemic began at the Huanan Seafood Wholesale Market, which many of the people who were infected earliest with SARS-CoV-2 had visited. The preprints contain genetic analyses of coronavirus samples collected from the market and from people infected in December 2019 and January 2020, as well as geolocation analyses connecting many of the samples to a section of the market where live animals were sold. Taken together, these lines of evidence point towards the market as the source of the outbreak — a situation akin to that seen in the epidemic of severe acute respiratory syndrome (SARS) in 2002–04, for which animal markets were found to be ground zero — says Kristian Andersen, a virologist at the Scripps Research Institute in La Jolla, California, and an author on two of the reports. “This is extremely strong evidence,” he says.

Did the coronavirus jump from animals to people twice?

However, none of the studies contains definitive evidence about what type of animal might have harboured the virus before it spread to humans. Andersen speculates that the culprits could be raccoon dogs, squat dog-like mammals used for food and their fur in China. One of the studies he co-authored2 suggests that raccoon dogs were sold in a section of the market where several positive samples were collected. And reports4 show that the animals can harbour other types of coronavirus.

Nevertheless, some virologists say that the new evidence pointing to the Huanan market doesn’t rule out an alternative hypothesis. They say that the market could just have been the location of a massive amplifying event, in which an infected person spread the virus to many other people, rather than the site of the original spillover.

“Analysis-wise, this is excellent work, but it remains open to interpretation,” says Vincent Munster, a virologist at the Rocky Mountain Laboratories, a division of the National Institutes of Health in Hamilton, Montana. He says that searching for SARS-CoV-2 and antibodies against it in blood samples collected from animals sold at the market, and from people who sold animals at the market, could provide more-definitive evidence of COVID-19’s origins. The number of positive samples from the market does suggest an animal source, Munster says. But he is frustrated that more-thorough investigations haven’t already been conducted: “We are talking about a pandemic that has upended the lives of so many people.”

Ground zero?

In early January 2020, Chinese authorities identified the Huanan market as a potential source of a viral outbreak because most people infected with COVID-19 at that time had been there in the days before they began to show symptoms, or were in contact with people who had been. Hoping to stem the outbreak, the authorities closed the market. Researchers then collected samples from poultry, snakes, badgers, giant salamanders, Siamese crocodiles and other animals sold there. They also swabbed drains, cages, toilets and vendors’ stalls in search of the pathogen. Following an investigation led by the World Health Organization (WHO), researchers released a report in March 2021 showing that all of the nearly 200 samples collected directly from animals were negative, but that around 1,000 environmental samples from the stalls and other areas of the market were positive.

A team in China including researchers at China’s Center for Disease Control and Prevention (CDC) has now sequenced genetic material recovered from those positive samples, and released the results in a preprint posted on 25 February1. The scientists confirm that the samples contain SARS-CoV-2 sequences almost identical to those that have been circulating in humans. Furthermore, they show that the two original virus lineages circulating at the start of the pandemic, called A and B, were both present at the market.

“It’s a nice piece of work,” says Ray Yip, an epidemiologist and a former director of the China branch of the US Centers for Disease Control and Prevention. “They’ve confirmed that the Huanan market was indeed a very important spreading location.”

As soon as the report from China had been posted online, Andersen and his colleagues rushed to post manuscripts they had been working on for weeks.