Genetic tracing at South China Seafood Market further supports animal origin of COVID-19

A new international collaborative study has published a list of wild animal species available in markets where SARS-CoV-2, the virus that caused the COVID-19 pandemic, likely emerged in late 2019. The study is based on a new analysis of metatranscriptomics data published by the Chinese Center for Disease Control and Prevention (CDC).

The data came from more than 800 samples collected from inside and outside the Huanan Seafood Wholesale Market since Jan. 1, 2020, and from viral genomes reported from early COVID-19 patients. The study was published Sept. 19 in the journal Cell.

“This is one of the most important datasets on the origins of the COVID-19 pandemic,” said co-corresponding author Florence Debarre of the French National Center for Scientific Research (CNRS). “We are very grateful that the data exists and that it has been shared.”

“This paper adds a new layer to the accumulating evidence that suggests the same scenario, that infected animals were introduced into a market in mid-to-late November 2019 and sparked the pandemic,” said co-corresponding author Christian Andersen of the Scripps Research Institute.

“We’ve taken the crucial data collected by the China CDC team and analyzed it in a new and rigorous way,” said co-corresponding author Michael Worobey of the University of Arizona. “This is an authoritative analysis of that data and how it fits with the rest of the vast body of evidence we have about how the pandemic began.”

On January 1, 2020, just hours after the animals were removed and the market closed, China CDC investigators returned to the market to take samples. They wiped down floors, walls, and other surfaces in the stalls, and then returned a few days later, focusing on surfaces such as cages in the stalls selling animals and carts for transporting the animals, and then took samples from drains and sewers.

They performed metatranscriptome sequencing of the samples, a technique that aims to obtain all the RNA sequences (and can also obtain DNA) from all organisms present in the sample (viruses, bacteria, plants, animals, and humans). The China CDC team, led by Liu Jun, published their data and findings in the journal Nature in 2023.

However, the paper did not reveal the exact identity of the possible intermediate host species found in the data. The China CDC shared the sequence data in a public and open repository.

A new data analysis published in Cell found that SARS-CoV-2 was present in some of the same stalls as wild animals sold at the market, including raccoon dogs (small, fox-like animals with raccoon-like markings) and civet cats (a small carnivorous mammal related to mongooses and hyenas).

In some cases, the SARS-CoV-2 virus and genetic material from these animals were even found on the same swab, and the exact animal species was identified by genotyping the mitochondrial genome in the samples.

“Many of the major animal species had been culled before the China CDC team arrived, so there is no direct evidence that animals were infected,” Debarre said. “There are traces of DNA and RNA from these animals in environmental samples, some in the stalls where SARS-CoV-2 was detected, which is what you would expect in a scenario where there are infected animals in the market.”

“These are the same kinds of animals that helped the first SARS coronavirus infect humans in 2002,” Worobey added. “This is the most dangerous thing we can do: playing with fire by capturing wild animals full of the virus and putting them in contact with humans living in big urban centers, where the high population densities make it easier for these viruses to take hold.”

The international team also conducted an evolutionary analysis of the earliest viral genomes reported in the pandemic, including these environmental sequences, to infer the most likely ancestral genotype of the virus that infected humans and caused the COVID-19 pandemic.

The results suggest that few or no humans were infected prior to the market outbreak, which is consistent with animal-to-human spillovers within the market, and possibly limited spillovers in the immediate upstream animal trade.

“In this paper, we show that market-associated sequences coincide with the emergence of markets,” Debarre said. “The main diversity of SARS-CoV-2 was present in markets from the beginning.”

A new study has listed animal species found to be coexistent or closely related to virus samples at a wet market as the most likely intermediate hosts for SARS-CoV-2. Raccoon dogs, which are susceptible to SARS-CoV-2 infection and transmitted SARS-CoV in 2003, were found to be the most genetically rich animal in samples taken from the wild animal stall at the market.

Genetic material from masked palm civets, which have also been linked to previous SARS-CoV outbreaks, was also found in the barn where SARS-CoV-2 RNA was found, and other species such as the white rat and Malayan porcupine were also found to be present in SARS-CoV-2 positive samples, along with a number of other species.

While the data cannot prove whether one or more of these animals were infected, the team’s analysis provides a clear list of species that were most likely carrying the virus, as well as genetic information that could help pinpoint their source.

The researchers highlight the importance of understanding the origins of the COVID-19 pandemic, especially in light of other recent spillover effects, such as the spread of avian influenza viruses in cattle in the U.S. “There is a lot of disinformation and misinformation circulating about the origins of SARS-CoV-2,” Worobey said.

“The reason it’s so important to find out this is because it has national security and public health implications not just in the United States but around the world. And the truth is, more than four years after the pandemic began, while there has been increased attention to laboratory safety, very little has been done to reduce the likelihood of a zoonotic scenario like this happening again.”