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A new study of genetic data from a market in Wuhan, China, says the data does not support the case that the pandemic started with illegally traded animals, touching off a new debate over samples that other scientists see as a critical piece of the puzzle. coronavirus reaches humans.
The new study, which examined the relative abundance of animals and viral material in swabs taken from surfaces in markets in early 2020, said it was difficult to draw conclusions about whether the virus samples came from infected live animals or just from incidental contamination.
But some outside experts say the analysis, posted online this week by the study’s author, Jesse Bloom, a virologist at the Fred Hutchinson Cancer Center, may have been affected by some unknown variables and decisions about how to filter the data.
For that reason, he said, the findings don’t have much impact on previous research. Samples from the market containing the animal’s genetic material and the virus, he said, were consistent with the possibility that an animal there — possibly a raccoon dog — had spread the virus to people, but did not prove that this had happened.
“I think there is a reasonable possibility that it was taken from an infected raccoon dog, but this does not prove where it came from,” said Frederic Bushman, a microbiologist at the University of Pennsylvania who specializes in analyzing samples like those taken from Wuhan. market, but who does not participate in any market studies. “I don’t think Bloom’s paper changed my mind.”
Chinese researchers wrote about the market data last year and then made the genetic sequence available this year, allowing an international team of scientists to study it. The team wrote in a report last month that based on the data, they could not identify animals that had transmitted the virus to humans.
But he said the data confirmed that animals believed to be infected with the virus, such as raccoon dogs and masked palm civets, small Asian mammals affected by the SARS outbreak two decades ago, were sold on the market in late 2019. The earliest Covid-19 patients were also work or shopping in the market.
Because the market is one of four places in Wuhan reported to be selling live animals that could spread the virus, scientists say it is unlikely that many of the early patients were linked to the market by chance. He said the genetic data also builds on other evidence, including that two early lineages of the virus are already on the market.
This week’s study takes a different approach to analyzing gene sequences.
Dr. Bloom investigated whether the amount of genetic material from the virus correlated with the amount of genetic material from susceptible animal species in the sample. If one species in the market is very responsible for destroying the virus, he said in an interview, he would expect to see a clear relationship between the amount of genetic material of the virus and the number of the species.
But the study found no such clear correlation. However, the strongest correlations were among fish sold in markets that could not be infected, an indication that infected people may have deposited viral material where the fish was.
Dr. Bloom said the findings suggest that the virus, also known as SARS-CoV-2, was circulating throughout the market when the swabs were collected in early 2020.
“In the same way we shouldn’t read too much into the fact that there’s a lot of SARS-CoV-2 mixed in with large bass and catfish samples, we shouldn’t read too much into the fact that there are raccoon dog samples. by reading SARS-CoV- 2,” said Dr. Bloom.
But outside experts say the various features of the samples can throw off efforts to link the animal material and the virus. International scientists said in the report that they had considered doing a similar analysis, but there was a risk of producing confusing results. Dr. Bloom admits that “it is an open question whether it is an informative thing to calculate at all.”
The genetic material of the virus breaks down quickly, said Christopher Mason, an environmental sampling specialist at Weill Cornell Medicine. Importantly, viral material can decay at a different rate than animal-derived material, making it difficult to compare samples collected within weeks of market closure.
It is possible that the fish closest to the virus is simply because the fish may have been frozen or refrigerated, causing the decay of the viral material in the sample, said Tom Wenseleers, an evolutionary biologist at KU Leuven in Belgium.
The latest analysis “confirms that looking at such correlations we don’t know much about the host species that could be the source of the pandemic,” said Dr. Wenseleers. This leaves scientists in the same situation as before, they say, with market data that does not provide conclusive evidence of a specific origin scenario.
The new study also examined swabs from market carts where the international team found traces of the virus along with the genetic signature of raccoon dogs, but no detectable genetic material from humans.
Dr. Bloom wrote that the swab contained only a small amount of viral material, and it is unclear why the Chinese researchers classified the swab as Covid-positive. The study said the swab was the only one that had raccoon dog genetic material in the amount of the virus.
However, some scientists say that the analysis of Dr. Bloom risks ruling out more Covid-positive swabs by setting the bar too high for the amount of animal genetic material in a sample.
Dr. Bushman, from the University of Pennsylvania, said that the threshold used in the analysis is “aggressive” and that it is best to compare the results obtained from a series of different cutoffs.
Using a more sensitive threshold, an international team of scientists identified various Covid-positive samples that contained the genetic material of raccoon dogs, as well as others that had genetic markers from various animals considered susceptible to the virus.
Alexander Crits-Christoph, a computational biologist formerly at Johns Hopkins University who helped lead the international team’s analysis, said the team is also looking closely at whether Chinese researchers were right to describe the swabs from the cars as positive for the virus.
He noted that several other swabs from the same stall were clearly positive for the virus. He said results from sampling elsewhere in the market also showed that unlike the swabs from the basket, most of the negative swabs showed no traces of the virus.
“This is an environmental sampling of a virus that is a tiny needle in a haystack,” said Dr. Crits-Christoph.
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