Scientists parse another clue to possible origins of Covid-19

There’s a tantalizing new clue in the hunt for the origins of the Covid-19 pandemic.

A new analysis of genetic material collected from January to March 2020 at the Huanan Seafood Market in Wuhan, China, has uncovered animal DNA in samples already known to be positive for SARS-CoV-2, the coronavirus that causes Covid-19. A significant amount of that DNA appears to belong to animals known as raccoon dogs, which were known to be traded at the market, according to officials with the World Health Organization, who addressed the new evidence in a news briefing on Friday.

The connection to raccoon dogs came to light after Chinese researchers shared raw genetic sequences taken from swabbed specimens collected at the market early in the pandemic. The sequences were uploaded in late January 2023, to the data sharing site GISAID, but have recently been removed.

An international team of researchers noticed them and downloaded them for further study, the WHO officials said Friday.

The new findings – which have not yet been publicly posted – do not settle the question of how the pandemic started. They do not prove that raccoon dogs were infected with SARS-CoV-2, nor do they prove that raccoon dogs were the animals that first infected people.

But because viruses don’t survive in the environment outside of their hosts for long, finding so much of the genetic material from the virus intermingled with genetic material from raccoon dogs is highly suggestive that they could have been carriers, according to scientists who worked on the analysis. The analysis was led by Kristian Andersen, an immunologist and microbiologist at Scripps Research; Edward Holmes, a virologist at the University of Sydney; Michael Worobey, an evolutionary biologist at the University of Arizona. These three scientists, who have been digging into the origins of the pandemic, were interviewed by reporters for The Atlantic magazine. CNN has reached out to Andersen, Holmes and Worobey for comment.

The details of the international analysis were first reported Thursday by The Atlantic.

The new data is emerging as Republicans in Congress have opened investigations into the pandemic’s origin. Previous studies provided evidence that the virus likely emerged naturally in market, but could not point to a specific origin. Some US agencies, including a recent US Department of Energy assessment, say the pandemic likely resulted from a lab leak in Wuhan.

What the samples show

In the news briefing on Friday, WHO Director-General Tedros Adhanom Ghebreyesus said the organization was first made aware of the sequences on Sunday.

“As soon as we became aware of this data, we contacted the Chinese CDC and urged them to share it with WHO and the international scientific community so it can be analyzed,” Tedros said.

WHO also convened its Scientific Advisory Group for the Origins of the Novel Pathogens, known as SAGO, which has been investigating the roots of the pandemic, to discuss the data on Tuesday. The group heard from Chinese scientists who had originally studied the sequences, as well as the group of international scientists taking a fresh look at them.

WHO experts said in the Friday briefing that the data are not conclusive. They still can’t say whether the virus leaked from a lab, or if it spilled over naturally from animals to humans.

“These data do not provide a definitive answer to the question of how the pandemic began, but every piece of data is important in moving us closer to that answer,” Tedros said.

What the sequences do prove, WHO officials said, is that China has more data that might relate to the origins of the pandemic that it has not yet shared with the rest of the world.

“This data could have, and should have, been shared three years ago,” Tedros said. “We continue to call on China to be transparent in sharing data and to conduct the necessary investigations and share results.

“Understanding how the pandemic began remains a moral and scientific imperative.”

CNN has reached out to the Chinese scientists who first analyzed and shared the data, but has not received a reply.

More data is out there

The Chinese researchers, who are affiliated with that country’s Center for Disease Control and Prevention, had shared their own analysis of the samples in 2022. In that preprint study posted last year, they concluded that “no animal host of SARS-CoV2 can be deduced.”

The research looked at 923 environmental samples taken from within the seafood market and 457 samples taken from animals, and found 63 environmental samples that were positive for the virus that causes Covid-19. Most were taken from the western end of the market. None of the animal samples, which were taken from refrigerated and frozen products for sale, and from live, stray animals roaming the market, were positive, the Chinese authors wrote in 2022.

When they looked at the different species of DNA represented in the environmental samples, the Chinese authors only saw a link to humans, but not other animals.

When an international team of researchers recently took at fresh look at the genetic material in the samples – which were swabbed in and around the stalls of the market – using an advanced genetic technique called metagenomics, scientists said they were surprised to find a significant amount of DNA belonging to raccoon dogs, a small animal related to foxes. Raccoon dogs can be infected with the virus that causes Covid-19 and have been high on the list of suspected animal hosts for the virus.

“What they found is molecular evidence that animals were sold at that market. That was suspected, but they found molecular evidence of that. And also that some of the animals that were there were susceptible to SARS-CoV2 infection, and some of those animals include raccoon dogs,” said Maria Van Kerkhove, WHO’s technical lead for Covid-19, in Friday’s briefing.

“This doesn’t change our approach to studying the origins of Covid-19. It just tells us that more data exists, and that data needs to be shared in full,” she said.

Van Kerkhove said that until the international scientific community is able to review more evidence, “all hypotheses remain on the table.”

More evidence for a natural origin?

Some experts found the new evidence persuasive, if not completely convincing, of an origin in the market.

“The data does point even further to a market origin,” Andersen, the Scripps Research evolutionary biologist who attended the WHO meeting and is one of the scientists analyzing the new data, told the magazine Science.

The assertions made over the new data quickly sparked debate in the scientific community.

Francois Balloux, director of the Genetics Institute at University College London, said the fact that the new analysis had not yet been publicly posted for scientists to scrutinize, but had come to light in news reports, warranted caution.

“Such articles really don’t help as they only polarise the debate further,” Balloux posted in a thread on Twitter. “Those convinced by a zoonotic origin will read it as final proof for their conviction, and those convinced it was a lab leak will interpret the weakness of the evidence as attempts of a cover-up.”

Other experts, who were not involved in the analysis, said the data could be key to showing the virus had a natural origin.

Felicia Goodrum is an immunobiologist at the University of Arizona, who recently published a review of all available data for the various theories behind the pandemic’s origin.

Goodrum says the strongest proof for a natural spillover would be to isolate the virus that causes Covid-19 from an animal that was present in the market in 2019.

“Clearly, that is impossible, as we cannot go back in time any more than we have through sequencing, and no animals were present at the time sequences could be collected. To me, this is the next best thing,” Goodrum said in an email to CNN.

In the WHO briefing, Van Kerkhove said that the Chinese CDC researchers had uploaded the sequences to GISAID as they were updating their original research. She said their first paper is in the process of being updated and resubmitted for publication.

“We have been told by GISAID that the data from China’s CDC is being updated and expanded,” she said.

Van Kerkhove said on Friday that what WHO would like to be able to do is to find the source of where the animals came from. Were they wild? Were they farmed?

She said in the course of its investigation into the pandemic’s origins, WHO had repeatedly asked China for studies to trace the animals back to their source farms. She said WHO had also asked for blood tests on people who worked in the market, as well as tests on animals that may have come from the farms.

“Share the data,” Dr. Mike Ryan, executive director of WHO’s health emergencies program, said Friday, addressing scientists around the world who might have relevant information. “Let science do the work, and we will get the answers.”