A recent study lists the wildlife species that were likely present at the market associated with the emergence of SARS-CoV-2, the virus that caused the COVID-19 pandemic, around late 2019. This research is founded on a new analysis of metatranscriptomic data from the Chinese Center for Disease Control and Prevention (CDC). The data, which includes over 800 samples collected from the Huanan Seafood Wholesale market starting January 1, 2020, also incorporates viral genomes from early COVID-19 patients.
A recent international collaborative study highlights the wildlife species likely found at the market where SARS-CoV-2, the virus responsible for the COVID-19 pandemic, most probably originated in late 2019. This study stems from a fresh analysis of metatranscriptomic data provided by the Chinese Center for Disease Control and Prevention (CDC). The researchers analyzed more than 800 samples retrieved from the Huanan Seafood Wholesale market starting on January 1, 2020, alongside viral genomes from early COVID-19 cases. The findings of this study have been published in the journal Cell on September 19.
“This is one of the most critical datasets regarding the COVID-19 pandemic’s origins,” states Florence Débarre, co-corresponding author from the French National Centre for Scientific Research (CNRS). “We are extremely thankful that this data exists and has been shared.”
“This paper contributes further to the mounting evidence pointing to the same conclusion: that infected animals were introduced into the market in late November 2019, triggering the pandemic,” remarks Kristian Andersen, co-corresponding author from Scripps Research.
“We have rigorously analyzed the valuable data collected by the Chinese CDC team,” says Michael Worobey, co-corresponding author from the University of Arizona. “This analysis serves as an authoritative examination of that data and its integration with the extensive evidence we possess regarding the pandemic’s origins.”
After the market closed and the animals were removed on January 1, 2020, Chinese CDC investigators collected samples from the market. They swabbed various surfaces, including floors and walls, and returned days later to focus on wildlife stalls. This included collecting samples from cages, carts, and drains and sewers.
The investigators conducted metatranscriptomic sequencing, a method designed to capture all RNA sequences (and can also detect DNA) from organisms present in the samples, ranging from viruses and bacteria to plants and animals, including humans. Although the Chinese CDC team, led by Liu Jun, published their findings in 2023 in the journal Nature, they did not fully resolve the specific animal species that could serve as potential intermediate hosts. The Chinese CDC made their sequencing data available in public repositories.
The recent analysis published in Cell indicates the presence of SARS-CoV-2 in stalls with wildlife at the market, including raccoon dogs (small fox-like animals resembling raccoons) and civet cats (small carnivorous mammals related to mongooses and hyenas). In certain instances, they found genetic material from both the SARS-CoV-2 virus and these animals on the same swabs. The exact animal species were determined through the genotyping of their mitochondrial genomes found in the samples.
“Many key animal species had already been removed by the time the Chinese CDC teams arrived, so we lack direct evidence of their infection,” Débarre comments. “We can see the DNA and RNA remnants of these animals in the environmental samples, and some are located in stalls where SARS-CoV-2 was also detected. This scenario aligns with the possibility of infected animals being present in the market.”
“These species are similar to those known to have enabled the original SARS coronavirus to jump to humans in 2002,” Worobey adds. “The most dangerous action is to introduce wild animals teeming with viruses into close contact with urban human populations, whose density facilitates virus transmission.”
The international research team also conducted an evolutionary analysis of the earliest viral genomes from the pandemic, including these environmental sequences. This analysis suggested there were very few, if any, humans infected before the market outbreak, supporting the idea of animal-to-human spillover occurring within the market. There may have also been some limited spillovers in the upstream animal trade.
“In this paper, we demonstrate that the sequences tied to the market align with the theory of market emergence,” Débarre states. “The primary diversity of SARS-CoV-2 was present in the market from the outset.”
The study identifies a short list of animal species in the wet market that were found in proximity to viral samples and could be the most likely intermediate hosts for SARS-CoV-2. The common raccoon dog, a species known to be susceptible to SARS-CoV-2 and that also carried SARS-CoV in 2003, was identified as the most genetically abundant animal in the market’s wildlife stalls. Genetic traces of masked palm civets, associated with the earlier SARS-CoV outbreak, were also discovered in a stall containing SARS-CoV-2 RNA. Additional species like the Hoary bamboo rat and Malayan porcupines were also found in SARS-CoV-2-positive samples, among many others.
While the data cannot conclusively prove whether any of these animals were infected, the team’s analyses present a clear list of the species that might have carried the virus, alongside genetic information useful for tracking their origins.
The researchers highlight the significance of understanding the origins of the COVID-19 pandemic, particularly in the context of recent spillovers like the emerging avian flu viruses in cattle in the United States. “There has been a lot of confusion about the origins of SARS-CoV-2,” Worobey explains. “Determining the truth is crucial for national security and public health, not solely in the United States but globally. Despite increased attention on lab safety since the pandemic began over four years ago, little has been done to diminish the risk of similar zoonotic occurrences in the future.”
