Where did COVID-19 originate? Saskatoon lab helps with genetic analysis that points to animal market

A team of scientists, including one in Saskatoon, say they have strong evidence that the COVID-19 virus jumped from infected animals to humans, rather than originating from a laboratory leak. 

The analysis of hundreds of genetic samples provides strong but circumstantial evidence that the pandemic’s origin is connected to the wildlife trade in the Huanan Seafood Wholesale Market, said Angie Rasmussen, a study co-author and virologist at the University of Saskatchewan’s Vaccine and Infection Disease Organization.

The study, published this fall in the journal Cell, shows the virus emerged at the market in Wuhan, China, at the same time as the pandemic began in the human population, suggesting it was the place of origin and linked to the live animals that were being sold there.

“It’s very difficult to explain any other way, besides that virus was brought there with those live animals and it spilled over, twice actually, into the human population at the market,” she said.

There had been two main theories about the origin of the COVID-19 pandemic, declared by the World Health Organization in March 2020. One was that the virus jumped from an infected animal to a human, most likely at the market; the second was that the virus was leaked from the Wuhan Institute of Virology. 

Even as the pandemic raged, determining its origins quickly became a high priority for the world’s top scientists. 

While other studies have looked into the presence of the virus at the market, this analysis examined the genetic samples that were there during a snapshot in time. This included samples of some animals that are known hosts and transmitters of coronaviruses such as raccoon dogs, bamboo rats and palm civets.

Strong likelihood of animal link, study says

The researchers were able to pinpoint exactly which species were present in hotspots where the virus spread. 

The analysis doesn’t prove the animals in those areas were infected. However, the proximity of COVID-19 samples to where their DNA was located means it’s a strong likelihood they were carriers, according to the study.

Dr. Lisa Barrett, an infectious disease specialist at Dalhousie University in Halifax, said the study is a good example of “very careful and pretty unbiased science” that could help prepare for future pandemic responses. It shows the importance of considering the density of animals in relation to humans and monitoring the wildlife trade, she said.

“If we don’t understand exactly how viruses spread and in what conditions they spread then we are always going to underestimate, or not estimate at all, where the next threat comes from,” she said.

“If you don’t know the why, history tends to repeat itself in the worst ways.”

Reading genetic clues

Rasmussen has been working with an international research team of top virologists since 2020, examining publicly available evidence to investigate the pandemic’s origins. Another Canadian scientist, evolutionary biologist and University of Arizona professor Michael Worobey, is also on the team. 

The team’s previous research, alongside other peer-reviewed studies, had determined the Huanan Market as the most likely place where the pandemic jumped to humans, specifically in association with the live animal trade.

Then in March 2023, a large dataset became quietly available online on a site where scientists share genetic sequences for research. The same data was used by Chinese scientists to publish a study in the journal Nature in 2023.

The research team quickly began analyzing the genetic clues collected by swabs from surfaces at the market.

The scientists say the new evidence makes the laboratory leak hypothesis incredibly difficult to support. 

All of the data analyzed in the recent study  — the early cases and proximity to the market, the location of animals, and the two independent spillovers into the human population, occurring weeks apart in late 2019 — points to COVID-19 originating at the market.

“None of that can be explained with a lab leak,” Rasmussen said.

For that to have happened, Rasmussen said someone would have had to get infected at the lab at the Wuhan Institute of Virology and then go to the market without infecting anybody else. The same exact thing would have had to happen again with the second lineage of the virus.

“When we’re talking about preventing future pandemics, we need to focus our resources on the problem that is much more likely to happen, than the hypothetical problem that is completely unsupported — and that would be the lab leak theory,” Rasmussen said.

Why the lab leak theory spread

The theory that the COVID-19 pandemic started after a lab leak began circulating in the early days of the pandemic. As more data became gradually available, top virologists — including Rasmussen’s team — argued the evidence was strongly pointing to the possibility of transmission from animals.

Timothy Caulfield, a professor at the University of Alberta and expert in health and science misinformation, said many people promoting the idea of a leak are trying to create broader distrust in scientific institutions.

“If you don’t believe the lab leak theory, you’re the enemy,” he said. “It really is viewed as a truism, that it has been definitively established that the lab leak is the source and if you believe otherwise you’re just simply wrong.”

Rasmussen and her colleagues have been targeted with online attacks as a result of their work.

“We’re accused of conducting a propaganda campaign essentially to cover up the real story of a lab leak. But that’s simply not true,” she said. 

Caulfield said the idea of a lab leak continues to spread widely, embraced by politicians in the U.S. and Canada and by people who feel compelled to back the beliefs of their political groups.

“The idea that this was an intentional action by some malevolent force, that’s also I think a part of, and closely associated with the lab leak theory, and one of the reasons that we continue to hear it today,” he said.