New genetic analysis finds clues to animal origin of COVID outbreak

The World Health Organization called Friday for Chinese health authorities to release genetic sequences of SARS-CoV-2 that recently disappeared from an international database, after an analysis of the data found it offered new clues that might point towards an animal origin for the COVID-19 pandemic.

The plea comes after a group of scientists outside China analyzed genetic sequences of SARS-CoV-2 viruses that had been initially posted late last month to the Global Initiative on Sharing Avian Influenza Data (GISAID) database by China’s Center for Disease Control and Prevention. The database is a site where scientists worldwide can access and share genetic sequencing and other data.

The data came from samples taken in early 2020 around the Huanan animal market in Wuhan, which investigations by U.S. and Chinese authorities had pointed to as a potential early epicenter for the outbreak.

Analysis of those samples found “molecular evidence” of animals like raccoon dogs at the market intermingled in swabs from the same spots that turned up the shedding from the virus itself in the market. 

Raccoon dogs are a species susceptible to SARS-CoV-2 infection that could potentially have served as an intermediate host, carrying the virus from bats or another source to humans. However, the samples only indicate that both raccoon dogs and the virus were present at the market; it is not direct proof that the species was the carrier.

File photo of a raccoon dog 
ARTERRA/Universal Images Group via Getty Images

“We need to make clear that the virus has not been identified in an animal in the market or in animal samples from the market, nor have we actually found the animals that infected humans. What this does is provides clues. It provides clues to help us understand what may have happened,” the WHO’s Maria Van Kerkhove told reporters Friday of the findings.

This new data prompted a meeting Tuesday of the WHO’s Scientific Advisory Group for the Origins of Novel Pathogens for the international scientists to present their analysis, as well as with the Chinese CDC researchers who had initially posted the data.

It is not clear why the records disappeared from the GISAID database after they were posted last month, or why Chinese researchers waited three years to release the data. 

The data had initially been posted by the Chinese researchers as part of work on a publication initially released last year as a preprint.

Researchers from China’s CDC released a preprint last year, which is now “under review,” that concluded that the Huanan market “might have acted as an amplifier” for spread of the virus introduced to the market by humans.

“We have been told by GISAID that the data from China CDC is being updated and expanded. But again, we have called on China CDC directly to make that data accessible in full. And so that remains absolutely fundamental,” Van Kerkhove said.

George Gao, the preprint’s lead author and the former head of the Chinese CDC, downplayed the significance of the new analysis to Science magazine. Gao said that it “had been known there was illegal animal dealing and this is why the market was immediately shut down.”

Gao declined to comment to CBS News on why the sequences were initially posted and then disappeared, deferring comment to GISAID. 

GISAID denied in a statement that they delete records from their database. Data “may from time to time become temporarily invisible” when revisions to improve or correct data are needed, GISAID said.

“To continuously improve the quality of data records, data contributors frequently update their records, e.g., when higher-resolution sequences or additional metadata become available, or when verification is required,” a GISAID representative said in an email.

Questions also are unanswered about the new analysis, which was first reported by The Atlantic. For example, Van Kerkhove declined to specify additional details about how and what other animals were identified in the sequencing analysis, deferring comment to the researchers.

French scientist Florence Débarre, named by The Atlantic as the researcher who initially spotted the sequences, did not respond to a request for comment. 

On Twitter, Débarre wrote that they were “not planning to communicate results before our report was finished. Finishing the report is my current priority.”

But even if Chinese health authorities repost the sequences they removed from GISAID, Van Kerkhove cautioned that far more research would be needed to understand if COVID-19’s origins could be conclusively linked to animals sold at the market. 

“We have repeatedly asked for studies to be done in other markets in Wuhan and in Hubei and across China. We have repeatedly asked for studies to trace those animals back to their source farms so that we can go back in time and actually look to see where the animals came from and if any testing had been done,” said Van Kerkhove.

While scientists have discovered evidence that suggests COVID-19 likely had zoonotic origins — that the virus emerged from animals that infected humans, similar to previous viruses — some elements of the U.S. intelligence community have concluded that it’s plausible the pandemic originated from a laboratory accident.

“Based on my initial analysis of the data, I came to believe, and I still believe today, that it indicates that COVID 19 more likely was the result of an accidental lab leak than a result of a natural spillover event,” former Trump administration CDC Director Dr. Robert Redfield told a hearing organized by House Republicans earlier this month.

In an interview with CBS News on Thursday, Dr. Anthony Fauci, who helped lead the U.S. response to the pandemic, said it’s possible we may never get a conclusive answer to the question of COVID’s origins.

“There really is no definitive proof,” he said. “We may not ever know precisely and definitively.”

Alexander Tin

CBS News reporter covering public health and the pandemic.

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