Covid-19: Analysis of samples from Wuhan’s Huanan market confirms its role as central site of early spread of the virus

CNN
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After extensive analysis of genetic material from hundreds of swabs taken from walls, floors, machinery and pipes inside the Huanan Seafood Wholesale Market in Wuhan, China – a site that has been described as an epicentre of the early spread of Covid-19 – scientists say they now know exactly which species of animals were in the same area where investigators also found the most positive samples of the virus that causes Covid-19.

Species present in areas where the highest number of SARS-CoV-2 samples were found include the raccoon dog, ashy bamboo rat, dog, European rabbit, Amur hedgehog, Malayan porcupine, Reeves’ muntjac, Himalayan marmot, and masked palm civet.

These new findings add to strong but circumstantial evidence that the SARS-CoV-2 virus jumped from infected animals to humans and that the market was a central location for early spread.

The researchers identified the animal species on the market using a technique called metagenomic sequencing, which reads all the genetic material in a sample and then sifts through it to understand where it came from.

The analysis, published Thursday in the journal Cell, does not prove that the animals were infected with the virus, but their DNA was found very close to the virus, sometimes in the same sample. It is therefore very likely that the animals were infected at the market.

Among the animals on the market, rabbits, dogs and raccoon dogs are known to be susceptible to COVID-19 infections. Raccoon dogs have also been shown to transmit the infection, making them strong candidates for being the first animals to transmit the virus to humans.

The international research team behind the study also used genetic material from the samples found on the market to conduct evolutionary analysis, a technique that helps them estimate when a virus first appeared and what its closest genetic relationship might be.

“This is essentially carbon dating viruses,” said the study’s lead author, Dr. Kristian Andersen, director of infectious disease genomics at the Scripps Translational Research Institute in La Jolla, California.

By understanding how quickly the virus that causes Covid evolves or mutates (it acquires about two genetic mutations per month), it is possible to roughly determine its age.

Researchers believe the virus that triggered the pandemic emerged between mid-November and mid-December 2019.

Their analysis shows that the SARS-CoV-2 virus on the market emerged at the same time as the broader pandemic virus, suggesting that they are one and the same virus.

If the virus had come from somewhere else and then traveled to the market where it spread — as the lab-leak theory of COVID-19’s origin suggests — the timing of the emergence of the virus found in the market would have been different than the emergence of the virus that caused the pandemic, Andersen said. The pandemic virus would have had an earlier birth date.

Other evidence points in the same direction.

Nearly a third of the first 174 people infected with Covid-19 had a link to the market, and many more with no direct link lived around the market in a city of 12 million people.

Andersen said that when he first saw how tight the grouping was, “I was flabbergasted.”

When he began reviewing the results of the hundreds of samples taken from the market in January 2020, “looking at what’s actually happening inside the market, I saw this cluster of environmental positivity, my brain was literally blown away. I was like, ‘I can’t believe what I’m seeing here,’” Andersen said.

Another important clue that suggests the market may be where the pandemic began is that both lineages of the virus that have been circulating since the early days of the pandemic — lineage “A” and lineage “B” — appear on swabs collected at the market.

Andersen said scientists have never had this much information, at this level of detail, for any previous pandemic.

The results closely match those of a similar analysis by Chinese scientists published in the journal Nature in 2023. The data used to conduct the analysis briefly became the subject of international intrigue when it was quietly published in March 2023 on GISAID, a site where scientists share the genetic sequences of viruses for research purposes.

Professor Florence Debarre, a CNRS researcher, discovered this data in 2023 and quickly alerted other scientists. She is also the lead author at Andersen on this new study.

“This adds additional weight to the evidence,” Debarre said of the new study. “Because as the data continues to accumulate, all the results keep pointing in the same direction, which is an origin linked to the wildlife trade in the Huanan market.”

This study adds to several important scientific articles from the same research group that have been published in major journals pointing to an animal origin for the start of the Covid-19 pandemic.

Andersen knows that many people will see his name on the new study on the origins of the Covid-19 pandemic and immediately dismiss its conclusions. He says he doesn’t care.

“They’re just going to look at the list of authors on the paper and say, ‘Oh, yeah, we can’t trust this,’ right? We don’t even need to read the paper,” Andersen said.

Andersen was one of the most prominent leaders of an international group of scientists who sifted through scientific evidence gathered in the early weeks of the pandemic, trying to understand how the global public health crisis began.

Andersen has been the target of government investigations and social media conspiracies because he changed his mind: After initially believing that SARS-CoV2 originated in a Wuhan lab that handled similar viruses, he published a scientific paper explaining why the virus that caused the Covid-19 pandemic likely came from animals that were infected and then passed it to humans — an event called a spillover.

Animal spillovers of this type are the cause of most pandemics.

Proponents of the lab leak theory believe that Andersen was pressured by top scientists at the National Institutes of Health to change his mind.

Andersen said none of this was true. He simply did what scientists do when faced with evidence that contradicts what they initially thought: he changed his hypothesis.

Debarre said she, too, initially believed the virus came from a lab.

“A laboratory origin is a possibility. It is a legitimate possibility for the origin of SARS-CoV-2 that had to be seriously considered and that we have considered,” Debarre said.

Andersen, she said, is well known as the first “lab whistleblower.”

“So we were all open to the idea of ​​a lab leak, except we’re scientists and we go where the data goes. And so far, all the available data and the different types of data all point in the same direction,” toward an animal spillover event that likely occurred at the Huanan market.

Lessons from past pandemics

Understanding the origin of SARS-CoV-2 is extremely important, not only for understanding what happened with Covid-19, but also for understanding how future pandemics might arise.

Andersen said a lot of work has been done in the wake of the pandemic to improve laboratory safety and the risk of accidental release of dangerous viruses, but much less focus has been placed on the wildlife and livestock trade, which continues to pose serious risks.

“How long has there been talk about the unregulated wildlife trade, which is worth over $50 billion a year in China,” Andersen said.

Andersen points out that they also found the H9N2 flu virus — another virus about to emerge — in samples taken from the Huanan market.

He said it was a frightening reminder that SARS-CoV-2 was not necessarily a special virus. It was simply a virus that happened to be in the right place at the right time.

The same scenario that happened in Wuhan in 2019 could happen today with the H5N1 bird flu virus in the United States on poultry and dairy farms. As long as the virus is spreading, he said, “it’s a game of chance.”

While Andersen acknowledges the need for stricter regulation around laboratory research on viruses, he believes more attention needs to be paid to animal markets.

“We also have another, even bigger problem, which is the unregulated wildlife trade,” Andersen said. “And that’s not even what we’re talking about.”