Researchers from the Chinese Centers for Disease Control and Prevention (China CDC) have released the eagerly awaited analysis1 of swabs taken from a wet market in Wuhan, China, in the early weeks of the COVID-19 pandemic as well as baseline data that the international research community has been clamoring for since the outbreak began.
Data confirms that swabs from the Huanan wholesale seafood market which has long been linked to the start of the pandemic contained genetic material from wild animals and tested positive for SARS-CoV-2. This suggests that it is possible that the animal could have been an intermediate host for the virus that spilled over and infected humans. However, scientists say the latest findings still fail to provide definitive proof that SARS-CoV-2 originated from animal-to-human transmission.
Still, scientists say the release of genomic data that has been stored in open repositories is crucial because it will enable further analysis that could offer clues about the origins of the pandemic. “It’s one of the most important datasets we’ve had since the outbreak of the pandemic,” says Florence Débarre, an evolutionary biologist at the French National Center for Scientific Research in Paris, who was part of the team that sparked controversy by publishing their own analysis of the Chinese CDC data last month . “They exist because the right things were done at the time.
Evolutionary virologist Jesse Bloom says that while the swabs taken in January 2020 provide useful information about what animals were in the market, earlier samples are needed to find the origin of the pandemic. “If we ever learn the exact origin of SARS-CoV-2, I suspect it will come from new information about cases or events in early December or November 2019 or earlier,” says Bloom, who is at Fred Hutchinson Cancer Research. Center in Seattle, Washington.
The Chinese team behind the latest report published a preprint version of their study in February 2022. The team which included Débarre, found swab data from the Chinese CDC in the GISAID online genomics database and published their own analysis on the Zenodo3 research repository. This report identified wild animal material in swabs that tested positive for SARS-CoV-2 and pointed to animals including raccoons as a species of interest.
Controversial study
The latest report lends weight to one of two competing theories about the origins of the COVID-19 pandemic. Debate raged over whether the pandemic had a natural origin, the virus was transmitted from animals to humans, or arose from a laboratory leak at the Wuhan Institute of Virology.
The Huanan market has been at the center of the natural origin theory because several of the first known cases of COVID-19 were linked to a market that sold animals known to host respiratory viruses called sarbecoviruses, which include SARS-CoV-2. in force and was not definitively excluded.
The latest paper, like the Zenodo report, details the mammalian genome sequences present in the market samples. The authors analyzed 60 samples that were positive for SARS-CoV-2 11 more than in the Zenodo report and another 112 swabs that were negative.
Wild animal species result covid
The findings support the natural-origin hypothesis, says the researcher, who was not involved in either study and wishes to remain anonymous because of the controversy surrounding the work on the origins of COVID. The presence of many wild animal species means that the virus that resulted in the COVID-19 pandemic could have spread, a scientist says.
Some of these species, such as raccoon dogs, have the potential to transmit SARS-CoV-2 infections, the source added. The study also offers clues about the role of the market in the emergence of the pandemic. In the early weeks of the outbreak, two lineages of SARS-CoV-2 dubbed A and B—were circulating. Initially, tests identified only lineage B in the market.
This led some researchers to conclude that the market may have merely acted as a site for an early “superspreader” event, rather than as a place of shedding of animals, since the A line is assumed to be more ancestral.
But a preprint released by China’s CDC last year identified the A lineage in one sample. “It’s the result that really made me shift, that really made me say, ‘Okay, it’s very likely that this will come out of the market,'” says Débarre. But he says some questioned whether the result was real. The new analysis confirms the presence of lineage A and resolves these doubts, he says.
David Relman, a microbiologist at Stanford University in California, agrees with the study authors’ assessment that the market may have acted as an amplifier of SARS-CoV-2 transmission. “It is just as possible that humans brought the virus to market as animals.”
False findings
Alice Hughes, a conservation biologist at the University of Hong Kong, is concerned about the quality of the analysis. In addition to genome fragments from animals, including raccoons, Hughes says the paper identifies genetic material from animals such as pandas, moles and chimpanzees. Since killing a panda attracts the death sentence in China, “there is absolutely no way there could be any trace of a panda in this market,” he says.
Odd results could be due to laboratory contamination or improper data processing that failed to remove false species identifications, Hughes says. “We have to be extremely careful with interpretation or putting too much faith in the paper.”
Débarre also questions aspects of the results. The China CDC authors used two methods of genomic analysis, one that searches all available genes and genomes, and another that targets specific sequences in the mitochondrial genome. The data do not clearly point to a specific animal as the intermediate host that transmitted the virus to humans. But the researcher, who wished to remain anonymous, says the results are back.
Written by: Vaishali Verma
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