Huanan Market Study Identifies Animals Likely to Have Carried SARS-CoV-2

Evidence from the Huanan seafood market

The virus responsible for COVID-19 seems to have made its initial jump into people from captive wild animals at Wuhan's Huanan seafood market. A new study has now pinpointed particular species that likely carried the virus.

This fresh assessment examines metagenomic RNA data gathered soon after the market was closed, adding to the growing body of evidence about the origins of SARS-CoV-2.

The earliest warning signs emerged in Wuhan, the capital of China's Hubei province, in late 2019. As well as the seafood and animal market, which has since closed, the city hosts the Wuhan Institute of Virology (WIV), whose researchers have investigated coronaviruses.

Studies indicate that SARS-CoV-2 was not created in a laboratory, yet its appearance in the same city as the WIV has prompted suspicion and extensive speculation. One widely discussed possibility is that, even if the virus developed naturally, it may have escaped after being collected from the wild by researchers.

There is little evidence supporting a laboratory leak, however. Many virologists consider it much more probable that the virus passed into humans from one of the numerous mammals at the Huanan market, where circumstances were favourable for a zoonotic spillover.

Seeking greater clarity, an international research group analysed data gathered by the Chinese Center for Disease Control and Prevention (CDC) in early 2020.

"This is one of the most important datasets that exists on the origin of the COVID-19 pandemic," says the study's senior author, evolutionary biologist Florence Débarre of the French National Centre for Scientific Research (CNRS).

"We're extremely grateful that the data exist and were shared."

Environmental sampling and genetic sequencing

Chinese CDC investigators entered the Huanan market on New Year's Day 2020, just hours after it had closed because of COVID. The animals had already been removed, but the researchers collected environmental samples.

Having initially swabbed surfaces in stalls used to keep animals, they returned several days afterwards to swab additional stalls, cages and carts. They also obtained samples from drains and sewers.

The team used metatranscriptomic sequencing to identify every RNA sequence from each organism found in the samples, as well as some DNA. They then compared these data with samples from early SARS-CoV-2 cases collected up to 14 February 2020.

The Chinese CDC researchers reported their results in Nature in 2023. They had collected more than 800 samples in total and, although they did not identify which animals might have been intermediate hosts for SARS-CoV-2, they made the sequencing data available through open-access repositories.

This allowed the new research team to conduct its analysis, identifying species in the samples by genotyping their mitochondrial genomes, the authors say.

Débarre, first author and microbiologist Alexander Crits-Christoph, and their colleagues detected evidence of the virus in stalls that had housed animals, including raccoon dogs and civets. In some cases, a single swab contained both animal genetic material and SARS-CoV-2.

"Many of the key animal species had been cleared out before the Chinese CDC teams arrived, so we can't have direct proof that the animals were infected," Débarre says.

"We are seeing the DNA and RNA ghosts of these animals in the environmental samples, and some are in stalls where SARS-CoV-2 was found, too," she adds. "This is what you would expect under a scenario in which there were infected animals in the market."

Raccoon dogs, civets and SARS-CoV-2

The researchers also carried out an evolutionary assessment of viral genomes from the earliest phase of COVID, looking for probable ancestors of the virus that triggered the pandemic. Their findings indicate that few, if any, people were infected before the outbreaks associated with the market.

"In this paper, we show that the sequences linked to the market are consistent with a market emergence," Débarre says. "The main diversity of SARS-CoV-2 was in the market from the very beginning."

Using their results, the authors compiled a shortlist of species at the market that were most likely to have acted as intermediate hosts.

They report that the common raccoon dog (Nyctereutes procyonoides) was the genetically most abundant animal in the samples. Genetic material from the masked palm civet (Paguma larvata) was also found in a stall containing SARS-CoV-2 RNA.

The researchers note that both species were associated with the original SARS outbreak, while common raccoon dogs are known to be susceptible to SARS-CoV-2.

"These are the same sorts of animals that we know facilitated the original SARS coronavirus jumping into humans in 2002," says ecologist Michael Worobey of the University of Arizona.

"This is the most risky thing we can do – take wild animals that are teeming with viruses and then play with fire by bringing them into contact with humans living in the heart of big cities, whose population densities make it easy for these viruses to take hold," Worobey adds.

Although the new study does not establish that any animals were infected with SARS-CoV-2, it provides leads that may support future investigations and further strengthens the case for the Huanan market as the starting point of COVID.

"This paper adds another layer to the accumulating evidence that all points to the same scenario: that infected animals were introduced into the market in mid- to late November 2019, which sparked the pandemic," says evolutionary biologist Kristian Andersen of the Scripps Research Institute in the US.

This matters both for retrospective research into the origins of COVID and for efforts to avert future pandemics.

"Since the pandemic started more than four years ago, although there has been an increased focus on lab safety, not much has been done to decrease the chance of a zoonotic scenario like this happening again," Worobey says.

The study was published in Cell.