Explained: What new data on SARS-CoV-2 says about Covid origin, what it doesn’t

The debate over the origins of SARS-CoV-2, the virus that causes Covid-19, is far from settled, but we now have a clearer understanding of one theory that has done the rounds since the beginning. Scientists on Tuesday published their arguments in favour of the theory that the virus possibly infected the first humans at Wuhan’s animal market.

The theory that it was accidentally leaked from a virology lab in Wuhan, on the other hand, is based on information that the US has not yet made public. Also on Tuesday, US President Joe Biden signed a bill directing the federal government to declassify as much information as possible about the origins of the virus.

What we do have at this point is a report of scientists’ analysis of samples collected from the Wuhan market. While the analysis does not conclusively establish their theory, the scientists make a strong case for their argument.

What data has been analysed, and where did it come from?

The data is three years old, and comes from environmental samples collected from various spots at the Huanan Wholesale Seafood Market in Wuhan. From the collection of samples to the latest analysis, the sequence of events was:

* In January and February 2020, shortly after the outbreak began, environmental samples were collected from cages, carts, drains and other locations in the market. Some of these samples were found to be positive for SARS-CoV-2.

* In February 2022, researchers from the Chinese Centre for Disease Control and Prevention published an analysis of this data on a preprint server. They reported that human genetic material was found in some of the samples positive for the coronavirus, but did not identify if genetic material from other animals was present.

* In July 2022, an international team of scientists published a paper in Science suggesting that infected animals were present at the Huanan market at the beginning of the pandemic. “However, we do not have access to any live animal samples from relevant species,” wrote the authors, several of whom are also co-authors of the latest analysis.

* On March 9, 2023, they found the data they were looking for on the website of GISAID, an international repository for SARS-CoV-2 genome sequences. The data was subsequently removed, but the team had by then downloaded it, leading to the analysis.

What did they find in the data?

The analysis has been published in the form of a report on Zenodo, an open repository operated by the European Organisation for Nuclear Research (CERN).

In the downloaded raw sequence data, the team found evidence of genetic material from a variety of wildlife species, some of which are known to be susceptible to SARS-CoV-2. In several samples, SARS-CoV-2 and animal RNA/DNA appeared together. Based on the IDs of the samples, the team was able to identify which part of the market each sample came from, and found that several of these came from a corner where wild animals were indeed being sold.

In a number of samples, genetic material from these animals, including raccoon dogs, was more abundant than human genetic material. Besides the common raccoon dog, the scientists were able to reconstruct mitochondrial genomes for the Malayan porcupine, Amur hedgehog, masked palm civet and hoary bamboo rat from wildlife stalls that were positive for SARS-CoV-2.

What does the co-occurrence of genetic material indicate?

It strongly indicates, but does not conclusively establish, that the DNA/RNA came from animals that were infected with SARS-CoV-2. The fact that animal genetic material was more abundant than that of humans lends credence to the theory of an animal intermediate host.

SARS-CoV-2 is believed to have originated in horseshoe bats, which infected one or more intermediate species that humans were in contact with, leading eventually to infection in humans. The findings indicate that the species whose genetic samples were identified from the downloaded data, including the raccoon dog, could have been the intermediate species.

Why is the evidence not conclusive?

Although the animal DNA/RNA and the virus RNA do occur together, it has not been established whether it was indeed these animals that shed the virus.

“If I wanted definitive proof that the virus came from an animal in the market, I would need to find the animal and test it to show that it had SARS-CoV-2,” leading virologist Gagandeep Kang, currently a professor at Christian Medical College, Vellore, told HT.

In this case, it is data from swabs, rather than animals directly, that shows virus and animal genetic material together. “The fact that you are finding them together is not proof that the virus originated from an infected animal,” Kang said.

It is possible, for example, that a human brought it into the market and an animal got infected. Kang cited various recorded cases of humans transmitting the virus to animals, including pet cats.

The newly published report, in fact, acknowledges that besides the samples in which animal genetic material was more abundant than that of humans, there were also many samples in which human genetic material was either abundant, or predominant with no evidence of non-human mammal DNA, “indicating that the SARS-CoV-2 virus at these sites was likely shed by humans”.

Despite these caveats, the team believes it has a strong case for its hypothesis.

“Although we cannot identify the intermediate animal host species from these data, a plausible explanation for the co-occurrence of the genetic material of SARS-CoV-2 and susceptible animals is that a subset of these animals were infected… This provides further support for the hypothesis that wildlife were the source of the first human SARS-CoV-2 infections,” the report said.

Where does all this leave the lab-leak theory?

Although the FBI and the US energy department have both said they believe the virus was accidentally released from the Wuhan Institute of Virology, which is not far from the wet market, the basis of this theory has not yet been made public.

The Wall Street Journal reported that the energy department’s conclusion, made with “low confidence”, is the result of “new intelligence”. The bipartisan bill signed by President Biden instructs the Office of the Director of National Intelligence to declassify intelligence related to the Wuhan Institute of Virology. Until this happens, there is no clarity on what that “new intelligence” is.

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