Scientist reviews data on raccoon dogs and Covid, emphasizing the unknowns

A new study of genetic data from a market in Wuhan, China, said the data did not support the case that the pandemic started with illegally traded animals, sparking fresh debate over samples that other scientists consider crucial pieces of the puzzle see how the coronavirus has reached people.

The new study, which examined the relative amounts of animal and viral material in swabs from surfaces on the market in early 2020, said it was difficult to draw conclusions about whether specific samples of the virus came from infected live animals or simply from accidental contamination .

But several outside experts said the analysis, posted online this week by study author Jesse Bloom, a virologist at Fred Hutchinson Cancer Center, was affected by a number of unknown variables and decisions about how to filter the data could have been.

For these reasons, they said, the results didn’t do much to sway their impression of previous studies. Samples from the market containing animal and viral genetic material, they said, were consistent with the possibility that an animal there — perhaps a raccoon dog — had transmitted the virus to humans, but didn’t prove it.

“I think there’s a pretty reasonable chance they picked up an infected raccoon dog, but that doesn’t prove that was the origin,” said Frederic Bushman, a microbiologist at the University of Pennsylvania who specializes in analyzing samples like those from Wuhan, but was not involved in any of the market studies. “I don’t think the Bloom paper changed my thinking that much.”

Chinese researchers wrote about the market data last year and then this year made the genetic sequences available for a team of international scientists to study. That team wrote in a report last month that they could not identify an animal that transmitted the virus to humans based on the data.

However, they said the data confirmed that animals thought to be susceptible to the virus, such as raccoon dogs and masked civet cats, a small Asian mammal implicated in the SARS outbreak two decades ago, rose in late 2019 were sold to the market. Many of these earliest Covid-19 patients also worked or shopped at the market.

Because the market was one of just four places in Wuhan selling live animals of the species that could plausibly spread the virus, the scientists said it was unlikely that so many early patients were linked to the market purely by accident . They said the genetic data also built on other evidence, including the fact that two early lineages of the virus were on the market.

This week’s study took 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 samples. If one species on the market was predominantly responsible for shedding the virus, he said in an interview, he would have expected to see a clear link between the amount of genetic material in the virus and the amount of that species.

However, the study found no clear associations of this type. Instead, the strongest correlations were among different fish sold on the market that could not have been infected, indicating that infected individuals had likely deposited viral material where the fish was located.

dr Bloom said the finding suggested the virus, also known as SARS-CoV-2, was widespread across the market at the time the swabs were taken in early 2020.

“Likewise, we shouldn’t read much into the fact that there is a bunch of SARS-CoV-2 mixed with largemouth bass and catfish samples, nor should we read much into the fact that there is a raccoon dog sample with a SARS-CoV-2 test,” said Dr. Bloom.

But outside experts said various features of the samples could frustrate efforts to correlate animal and viral material. The international scientists said in their report that they had considered conducting a similar analysis, but that there was a risk of producing misleading results. dr Bloom acknowledged that “it’s an open question whether the calculation is meaningful at all.”

Genetic material from the virus breaks down rapidly, said Christopher Mason, an environmental sampling specialist at Weill Cornell Medicine. Crucially, viral material may break down at a different rate than material from animals, making it difficult to compare them in samples collected over the weeks after the market closed.

It could be that fish was most closely associated with the virus simply because the fish was likely frozen or refrigerated, which slowed the decay of viral material in these samples, said Tom Wenseleers, an evolutionary biologist at KU Leuven in Belgium.

The latest analysis “confirms that looking at these types of correlations says next to nothing about which host species might have been a plausible source of the pandemic,” said Dr. Wenseleers. This leaves the scientists in the same position as before, he said, with market data offering no conclusive evidence for any particular origin scenario.

The new study also looked closely at a swab from a cart at the market, in which the international team had found traces of the virus alongside genetic signatures from raccoon dogs, but no detectable human genetic material.

dr Bloom wrote that the swab contained only a tiny amount of viral material and that it was not clear why Chinese researchers had classified the swab as Covid positive. His study said the swab was the only one that contained significant amounts of raccoon dog genetic material with traces of the virus.

However, some scientists said that Dr. Bloom’s analysis risked rejecting other Covid-positive swabs by setting the bar too high for the amount of animal genetic material in a sample.

dr Bushman of the University of Pennsylvania said the threshold used in the analysis was “aggressive” and that it was best to compare results obtained from a number of different thresholds.

Using a more sensitive threshold, the international team of scientists identified several Covid-positive samples that contained genetic material from raccoon dogs, as well as others with genetic signatures from different animals thought to be susceptible to the virus.

Alexander Crits-Christoph, a computational biologist who formerly worked at Johns Hopkins University and helped lead the international team’s analysis, said the team also carefully checked whether the Chinese researchers were correct in testing the swab from the car as positive for described the virus.

He found that a number of other swabs from the same barn were clearly positive for the virus. He said results from sampling elsewhere in the market also indicated that most of the truly negative swabs contained no trace of the virus at all, unlike the swabs from the cart.

“This is an environmental sampling of a virus that is a tiny needle in a haystack,” said Dr. Crits-Christoph.