After an in-depth analysis of the genetic material from hundreds of swabs taken from the walls, floors, machines and drains inside the Huanan Seafood Wholesale Market in Wuhan, China — a site that’s been described as an epicenter of 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 the virus that causes Covid-19.
Species present in the areas where the highest numbers of SARS-CoV2 samples were found include raccoon dog, hoary bamboo rat, dog, European rabbit, Amur hedgehog, Malayan porcupine, Reeves’s muntjac, Himalayan marmot, and masked palm civet.
The new findings add to strong, but circumstantial evidence that the SARS-CoV2 virus jumped from infected animals to humans and that the market was a central site of early spread.
The researchers identified the species of animals at the market through a technique called metagenomic sequencing, which reads all the genetic material present in a sample and then sifts through to understand where it came from.
The analysis, which published Thursday in the journal Cell, doesn’t prove that the animals were infected by the virus, but their DNA was found very near the virus, sometimes on the same swab. That means it’s a strong possibility the animals were infected at the market.
Of the animals present at 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 a strong candidate to be the animals that first passed the virus to humans.
Studying the age of viruses
The international research team behind the study also used the genetic material from samples found in the market to conduct an evolutionary analysis, a technique that helps them estimate when a virus first emerged and what its closest genetic relation might be.
“It’s basically carbon dating viruses,” said senior study author Dr. Kristian Andersen, who is director of infectious disease genomics at Scripps Translational Research Institute in La Jolla, California.
By understanding how quickly the virus that causes Covid changes, or mutates — it acquires about two genetic mutations a month — it’s possible to figure out approximately how old it is.
The researchers believe that the virus that sparked the pandemic emerged sometime between mid-November and mid-December 2019.
Their analysis shows that SARS-CoV2 virus present at the market emerged at the same time as the virus from the larger pandemic, suggesting they are one and the same.
If it had come from somewhere else first, and then traveled to the market where its spread was amplified — as a 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 an earlier birthdate.
Other lines of evidence point in the same direction.
Almost one-third of the first 174 people who got Covid-19 had a connection to the market, and many others without a direct connection lived around the market, within a city of 12 million people.
Andersen said when he first saw how tight this clustering was, “I was flabbergasted.”
When he started looking at the results of the hundreds of swabs taken in the market in January 2020, “looking at what’s actually happening inside the market, and I saw that clustering of environmental positivity, my brain was literally blown. I was like, I can’t believe what I’m looking at here,” Andersen said.
Another important clue that the market might be where the pandemic started is that both lineages of the virus that were circulating from the earliest days of the pandemic — the “A” lineage and the “B” lineage — are on the swabs collected at the market.
Accumulating evidence of animal origin
Andersen said scientists have never had this much information, at this level of detail, for any previous pandemic.
The findings closely align with a similar analysis performed by Chinese scientists that was published in the journal Nature in 2023. The data used to conduct the analysis was briefly the subject of international intrigue when it was quietly posted to GISAID in March 2023, a site where scientists share the genetic sequences of viruses for research.
Professor Florence Debarre, a researcher at the French National Centre for Scientific Research (CNRS), discovered the data in 2023, and quickly alerted other scientists. She is also a senior author with Andersen on this new study.
“What this adds is a greater weight of evidence,” Debarre said in an interview about the new study “Because as data keep accumulating, all the results still go in the same direction, which is an origin linked to wildlife trade in the Huanan market.”
This study comes on top of several important scientific papers by 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 a lot of people will see his name on the new study about the origins of the Covid-19 pandemic and immediately dismiss its findings. He says he doesn’t care.
“They will just look at the author list on the paper and say, ‘Oh, yeah, we can’t trust any of this,’ right? So we don’t even need to read the paper,” said Andersen.
Andersen has been one of the most prominent leaders of an international group of scientists who have been sifting through scientific evidence collected in the early weeks of the pandemic, trying to understand just how the global public health crisis started.
Andersen has been the intense focus of government investigations and social media conspiracies, because he changed his mind: After initially believing that SARS-CoV2 came from a lab in Wuhan, that was manipulating similar viruses, he published a scientific paper explaining why the virus that caused the Covid-19 pandemic probably came from animals who were infected and then passed it to humans — an event called a spillover.
Animal spillovers like these are the way most pandemics begin.
Proponents of the lab leak theory think that Andersen was pressured by top scientists at the National Institutes of Health to change his thinking.
Andersen said none of that is true. He simply did what scientists do when presented with evidence that contradicts what they initially thought: He changed his hypothesis.
Debarre says she, too, originally believed that the virus emerged from a lab.
“A lab origin is a possibility. It’s a legitimate possibility for the origin of SARS-CoV2 that needed to be seriously considered, and that we did consider,” Debarre said.
Andersen, she said, is well known as the original “lab leaker.”
“So we were all open to the idea of a lab leak, except that we are scientists, and we go where the data go. And so far, all the data that are available and different types of data all point in the same direction,” toward an animal spillover event that likely happened in the Huanan market.
Lessons of past pandemics
Understanding the origin of SARS-CoV2 is hugely important, not only to understanding what happened with Covid-19, but also understanding how future pandemics will likely come our way.
Andersen said much work has been done in the wake of the pandemic to improve lab safety and the potential for the accidental release of dangerous viruses, but there’s been much less focus on the trade of wild and farmed animals, which continues to pose serious risks.
“How much has been talked about the unregulated wildlife trade, which is a 50-plus billion dollar annual trade in China,” Andersen said.
Andersen points out that they also found H9N2 flu virus — another virus poised for emergence — in the samples taken from the Huanan market.
He said it’s a chilling reminder that SARS-CoV2 wasn’t special, necessarily. It was just a virus that was in the right place at the right time.
The same scenario that happened in Wuhan in 2019 could be playing out now 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 agrees that there needs to be more regulation around lab research of viruses, he said more attention needs to be given to animal markets.
“We also have a bigger boogie monster right in front of us, which is unregulated wildlife trading,” Andersen said. “And that’s not even being discussed.”
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