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Debate deepens over Wuhan wet market’s role in kickstarting the pandemic

The troubled history of wet markets

Even before COVID-19, Huanan and other wet markets were notorious public-health threats because of their potential as breeding grounds for new pathogens. Most notably, a Chinese marketplace was found to be ground zero for the SARS outbreak in 2002, and other wet markets have been linked to several outbreaks of bird flu in recent years.

In fact, researchers in China were already conducting routine surveys of live animals sold at the Huanan market. In response to outbreaks of a deadly tick-borne disease, a team of scientists had been investigating four markets in Wuhan—including Huanan—every month between May 2017 and November 2019. That data, published in Scientific Reports last year, has since become a valuable resource for scientists trying to understand the origins of SARS-CoV-2.

The team revealed that these markets housed nearly 48,000 caged wild animals belonging to 38 species, almost all of which were sold alive and stacked in cramped, unhygienic conditions perfect for virus mingling and transmission. All of the wildlife trade the scientists surveyed at these four markets was illegal. Many vendors sold protected species, and none held the required certificates stating the source of the animals or that they were free of disease.

This survey was one of the core pieces of evidence used in the new Science papers, along with a study jointly conducted by the WHO and China, which published in March last year, and a leaked report from the Chinese CDC dated January 22, 2020, that described some of the environmental samples collected at Huanan in early 2020.

Their analyzes show that most of the environmental samples that tested positive for SARS-CoV-2 were concentrated in the southwestern section of Huanan market, where vendors illegally sold live animal species susceptible to the virus—including raccoon dogs, red foxes, and bamboo rats. —in the weeks leading up to the early outbreaks. A single stall in that part of the market—stall #29—yielded five positive samples, and four of them were from items apparently associated with the wildlife trade: a metal cage, a machine for removing hair or feathers, and two carts for transporting animals.

The most likely explanation is that the virus in those samples was shed by an infected animal, indicting a spillover event in the market, says Edward Holmes, a virologist at the University of Sydney in Australia and a co-author of both Science papers.

But scientists hunting for COVID-19’s origins are frustrated that animals infected with a progenitor of SARS-CoV-2 remain elusive. When Huanan was suspected to be the source of the early outbreak, vendors illegally selling live wildlife disappeared with their animals. Several research groups raced to track down the infected wildlife without success.

Between January 7 and 18, 2020, Tian Junhua of the Wuhan CDC and his colleagues collected samples from wild animals near the city, including 15 raccoon dogs from farms that supplied Huanan and hundreds of bats; they found no trace of SARS-CoV-2. Scientists who were part of the WHO-China joint study also failed to find the virus when they analyzed more than 600 samples from farms in Hubei Province that supplied the Huanan market. Their analysis of nearly 2,000 samples belonging to more than two dozen species of wildlife from the southern provinces of Yunnan, Guangdong, and Guangxi that are home to numerous coronavirus-carrying bats also failed to yield samples of SARS-CoV-2.

Rosenberg isn’t surprised the researchers came up empty handed. He says tracking down the source of a new zoonotic disease is like looking for a needle in a haystack, and it’s especially challenging—if not impossible—when the infection of an animal population might be only floating.

A cloudy genomic picture

Without homing in on infected wildlife, one way to provide spillover at Huanan is to find the animal virus in the market that started the pandemic. If COVID-19 emerged when a virus jumped from an animal to a human at Huanan, then it should be possible to find in the market a progenitor of SARS-CoV-2 that is different from the human counterparts. But such a virus hasn’t been found.

In a study posted in February that has not yet been peer reviewed, a team led by George Gao, director of the Chinese CDC who just stepped down this week, unveiled a complete analysis of the 800 environmental samples from Huanan, including sewage wells, the floors, walls, freezers, and animal cages. Two thirds of the 64 positive samples came from the southwestern section of the market where live wildlife were sold. Four of those positive samples—none from Stall 29 which Holmes and his colleagues believe was where spillover took place—yielded complete genomic sequences that are identical to human SARS-CoV-2. Therefore, the Chinese team concluded that the viruses were shed by humans, rather than animals, bolstering the case that the market was an amplifier of the virus, not the source.

Many scientists are skeptical. It’s hard to verify the conclusion since the data Gao’s team used are not publicly available, says Andrew Rambaut, an evolutionary biologist at the University of Edinburgh in UK and a co-author of both Science papers. He notes that positive samples from the market environment contain genetic materials from animals, and he would want to know which species they were, the quantity of genetic material, and how that might correlate with the location of the wildlife stalls.

Moreover, authors on the two new Science papers think they’ve found genetic clues to spillover happening at the market.

Joel Wertheim of the University of California, San Diego, led a team that scrutinized nearly 800 early viral sequences that were sampled from around the globe before February 2020. They found two forms of SARS-CoV-2, dubbed A and B, that differ by just two units of genetic code. Crucially, these forms gave rise to two gigantic explosions of genomic diversity in the early pandemic. Weitherm calls this “a telltale sign” that two closely related versions of the virus jumped from animals to humans on two separate occasions.

Both lineage A and B turned up in some of the Huanan environmental samples that the Chinese CDC team analyzed, notes Michael Worobey, an evolutionary biologist at the University of Arizona in Tucson and also a co-author of both Science papers. If the two-jumps theory holds water, then it’s most likely both jumps took place at the market—a hypothesis he regards as more likely than a scenario in which two individuals infected from outside Huanan brought the viruses to the same market.

“It’s a cannonball through the whole of this idea that the Huanan market was just an amplifying event,” says Worobey.

But other work suggests that a third virus lineage that emerged in October at the latest is the one that gave rise to all SARS-CoV-2 genomes. In a study published in Bioinformatics in March, a team led by Sudhir Kumar of Temple University in Philadelphia analyzed more than a million genomic sequences of SARS-CoV-2 collected from around the world and concluded that there was only one common ancestor, indicating just one jump.

These studies used different methods to infer viral evolution based on observed genomic sequences, and both approaches have uncertainties, so several scientists approached by National Geographic say that their conclusions should be taken with a grain of salt.

But while the precise location of the spillover remains murky, most virologists and infectious-disease experts agree that China’s wildlife trade played a central role in igniting the pandemic wildfire. There is, says Frutos, an urgent need to look at risks across the entire supply chain.

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