Samples collected at the Huanan Seafood Wholesale Market in Wuhan, China, in the early weeks of the COVID-19 pandemic are of limited value for pinpointing which animal species — if any — infected people at the market, according to a new analysis1.
Two previous analyses of the data described genetic material from various wild animals, suggesting it was possible that these animals could have passed the virus to people at the market. The new analysis attempts to identify the specific animal responsible for the spillover — but comes up empty.
“I would basically describe this as a negative result,” says Jesse Bloom, a virologist at the Fred Hutchinson Cancer Center in Seattle, Washington, who conducted the latest analysis, which has not yet been peer reviewed. “It doesn’t say either way whether there were ever any infected animals in the market,” he says. “It doesn’t say what the origin of the virus is.”
Florence Débarre, an evolutionary biologist at the French national research agency CNRS in Paris, who co-authored the first report on the animal sequences says that the latest analysis could never have answered the question of which animal hosts shed the viral material detected, because there was so much virus being shed by humans by the time the samples were collected.
Bloom analysed data on genetic material detected in swabs collected at the Huanan market by scientists at the Chinese Center for Disease Control and Prevention (China CDC) after the market was closed on 1 January 2020 owing to concerns about an emerging virus, which was later named SARS-CoV-2. In February 2022, scientists at the China CDC published a preprint paper2 that revealed the presence of SARS-CoV-2 in a small number of environmental samples — from stalls, floors and walls — taken at the market. But the China CDC did not report on animal sequences detected in those samples and did not release the underlying data.
Bloom’s analysis is the third study in two months to focus on the genetic sequences of animals in the samples. The first report — posted in March by an international team of researchers including Débarre who discovered a subset of the China CDC data on GISAID, an online public data repository — found evidence of wild animals in samples positive for SARS-CoV-23. The genomic sequences identified included those of raccoon dogs (Nyctereutes procyonoides) and hoary bamboo rats (Rhizomys pruinosus) — species that could have been intermediate hosts of the virus. In the second, published in Nature in April, scientists at the China CDC provided their own analysis4 of the animal sequences. The list of animals was different, but did include notable species such as bamboo rat and raccoon dog. They also posted the complete data set online.
Virologist George Gao from the China CDC, and lead author of the Nature study, says the new analysis yielded results similar to the China CDC’s work.
Signs of infection
Neither of the two previous reports on the animal sequences could confirm that animals were infected with SARS-CoV-2. Bloom’s analysis also supports these results.
Bloom investigated whether environmental swabs rich in viral sequences were associated with genetic material from a particular animal, which could be a sign of infection. But there was no such association that made sense, says Bloom.
In fact, the strongest associations were with species, such as fish, cows and goats, that SARS-CoV-2 is not known to infect, says Bloom. “This doesn’t provide any more insight on whether raccoon dogs, or any other animal there, were or were not ever infected with SARS-CoV-2,” he says. The swab data merely confirm that the virus was widespread at the market, he says.
“We always knew that we could not definitively say if raccoon dogs were carrying [the virus] or if there had just been a commingling of the DNA,” says Alice Hughes, a conservation biologist at the University of Hong Kong, who was not involved in any of the studies.
Making inferences based on precise amounts of genetic material found in environmental samples is problematic, says Hughes. “Some species are just going to be shedding more DNA than others,” she says, because of the animals’ size, their behaviour or how they are handled and processed at the market. Sequencing can also introduce bias, says Hughes, because some genetic sequences amplify better than others.
Still, Débarre emphasises the latest analysis is important, because it independently confirms that specific wild animals capable of being infected with SARS-CoV-2 were at the market before its closure. It also shows that those animals were located in the part of the market linked to the most human cases, which, she says, adds weight to the hypothesis that the pandemic had a natural origin.
More samples needed
Débarre says that more could be learnt if any of the original samples remain. For example, targeted sequencing of the virus might give a clearer picture of the early evolutionary history of the virus.
Hughes says that frozen animal carcasses or blood samples collected from people in late 2019 could hold some answers if any such samples exist. New surveys looking for SARS-CoV-2 antibodies in blood collected from people working in the supply chain of the wild-animal trade are unlikely to be useful, she says, because of the subsequent widespread SARS-CoV-2 infections in the Chinese population.
Bloom says that the existing swab data might yet yield further insights. For example, the sequences could reveal which wild or farmed populations the animals at the market came from. That information could be used to target geographical locations that researchers should investigate for the presence of coronaviruses related to SARS-CoV-2.
Gao says that the China CDC has no additional data from the early swabs. “We do not have anything of the earlier sequencing data from China CDC that have not [been] shared with the world,” he says. “The origin of the virus is a scientific question and remains elusive.”