After a thorough analysis of the genetic material from hundreds of swabs taken from the walls, floors, machinery and drains at the Huanan Seafood Wholesale Market in Wuhan, China - a location described as an epicenter of the early spread of Covid-19 - scientists say they now know exactly which animal species were in the same area where researchers also found the most positive samples for the virus that causes Covid-19.
Species found in the areas with the highest numbers of SARS-CoV-2 samples include the raccoon dog, gray bamboo rat, dog, European rabbit, Amur hedgehog, Malayan porcupine, Reeves' muntjac, Himalayan marmot, and the masked palm civet.
The new findings add to the strong but indirect evidence that the SARS-CoV-2 virus was transmitted from infected animals to humans and that the market was an important site for early spread.
The researchers identified the species on the market using a technique called metagenomic sequencing, which involves reading all the genetic material in a sample and then sifting through it to determine where it came from.
The analysis, published Thursday in the journal Cell, does not prove the animals were infected with the virus, but their DNA was found very close to the virus, sometimes on the same swab. That means there is a high probability that 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 transmitted the virus to humans.
Studying the age of viruses
The international research team behind the study also used genetic material from samples found on the market to perform an evolutionary analysis. This technique helps them estimate when a virus first emerged and what its closest genetic relative might be.
"It basically means that viruses are being dated using carbon dating," said lead researcher Dr. Kristian Andersen, director of the infectious disease genomics division at the Scripps Translational Research Institute in La Jolla, California.
By understanding how quickly the virus that causes Covid changes, or mutates (it undergoes about two genetic mutations per month), it may be possible to estimate how old it is.
Researchers believe the virus that caused the pandemic emerged sometime between mid-November and mid-December 2019.
Their analysis shows that the SARS-CoV-2 virus present in the market emerged at the same time as the virus from the larger pandemic, suggesting that they are one and the same virus.
If it had first emerged from somewhere else and then traveled to the market where its spread was amplified - as one lab-leak theory about the origins of Covid-19 suggests - the timing of the virus's emergence in the market would have been different from the emergence of the virus that caused the pandemic, Andersen said. The pandemic virus would have an earlier birth date.
Other lines of evidence point in the same direction.
Nearly a third of the first 174 people infected with Covid-19 had a connection to the market. Many others without a direct connection lived near the market in a city of 12 million people.
Andersen said that when he first saw how dense this clustering was, "I was astonished."
When he went to look at the results of the hundreds of swabs on the market in January 2020, "I looked at what was actually happening in the market and I saw this accumulation of positive environmental influences, and my brain was literally blown away. I thought, 'I can't believe what I'm seeing here,'" Andersen said.
Another important clue that the market could be the place where the pandemic started is that both virus lines that have been circulating since the early days of the pandemic - the "A" line and the "B" line - are present on the swabs collected from the market.
Collecting evidence of animal origin
According to Andersen, scientists have never before had so much information and detail about such a pandemic.
The findings closely mirror those of a similar analysis conducted by Chinese scientists and published in the journal Nature in 2023. The data used in the analysis was briefly the subject of international intrigue when it was quietly posted in March 2023 to GISAID, a site where scientists share the genetic sequences of viruses for research.
Professor Florence Debarre, a researcher at the French National Center for Scientific Research, discovered the data in 2023 and quickly alerted other scientists. She is also a senior author at Andersen on the new study.
"What this adds is a greater weight of evidence," Debarre said of the new study. "Because as the data continues to pile up, all the results continue to point in the same direction, which is an origin that is linked to the wildlife trade in the Huanan market."
This study follows several major scientific papers from the same research group 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 findings. He says he doesn't care.
"They 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 have to read the paper," Andersen said.
Andersen is one of the leading figures in an international group of scientists who have been reviewing scientific evidence from the early weeks of the pandemic to try to understand how the global public health crisis emerged.
Andersen has become the focus of government investigations and social media conspiracy theories because he has 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 likely came from animals that were infected and then passed it on to humans - an event called a spillover.
Such transmission effects to animals are the cause of most pandemics.
Proponents of the lab leak theory believe Andersen was pressured by top scientists at the National Institutes of Health to change his thinking.
Andersen said that none of this is true. He simply did what scientists do when confronted with evidence that contradicts what they originally thought: he changed his hypothesis.
Debarre says she too was initially convinced that the virus originated in a laboratory.
"A lab origin is a possibility. It is a legitimate possibility for the origin of SARS-CoV-2 that should be seriously considered and that we did consider," Debarre said.
Andersen, she said, is known as the original "lab leaker."
"So we were all open to the idea of a lab leak, except we are scientists and we go where the data goes. And so far, all the available data and different types of data all point in the same direction," to an animal spillover event that likely occurred at the Huanan market.
Lessons from previous pandemics
Understanding the origins of SARS-CoV-2 is of paramount importance, not only to understand what happened with Covid-19, but also to understand what future pandemics might mean for us.
According to Andersen, much work has been done in the wake of the pandemic to improve laboratory safety and reduce the risk of unintentional spread of dangerous viruses. However, much less attention has been paid to the trade in wild and farmed animals, which still poses serious risks.
"There has been a lot of talk about the unregulated wildlife trade, which is worth more than $50 billion a year in China," Andersen said.
Andersen points out that in the samples taken at the Huanan market, they also found the H9N2 flu virus, another virus that is on the verge of emerging.
He said it was a chilling reminder that SARS-CoV-2 wasn't necessarily special. It was just a virus that was in the right place at the right time.
The same scenario that played out in Wuhan in 2019 could now play out 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."
Andersen agrees that there needs to be more regulation around laboratory testing of viruses, but he also says more attention needs to be paid to animal markets.
"We also have an even bigger bogeyman in front of us, which is the unregulated wildlife trade," Andersen said. "And that's not even being talked about."
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