Part 1

It remains of the greatest mysteries in virology, despite the clustering of early cases at the now-infamous Huanan Seafood Wholesale Market in Wuhan, China. This seemed like a smoking gun—after all, the 2002 SARS-CoV-1 outbreak in China was confidently tied to masked palm civets being sold at Xinyuan Market in Guangdong Province, shortly after the outbreak began. And yet, more than six years after the onset of the pandemic, the World Health Organization's (WHO) judgement on the origin of the pandemic remains:

The Huanan Seafood Wholesale Market, examined

On September 19, 2024, a scientific paper was published in the journal Cell, identifying a specific stall on the western side of the market with a stunning 30% SARS-CoV-2 test positivity rate, on samples collected from surfaces at the stall, including samples from animal carts/cages and a hair/feather removal machine. Critically, the western side of the Huanan Market is where the earliest COVID-19 cases in humans were clustered, and a whopping 30% of surface samples from this stall tested positive despite the fact that all samples from most stalls tested negative.

What animals were sold at this stall? Citing genetic evidence from the swab samples, the Cell paper lists dogs, raccoon dogs, rabbits, Amur hedgehogs, Malayan porcupines, hoary bamboo rats, Himalayan marmots, Reeves’s muntjac deers, and masked palm civets. Sound familiar?

However, the paper makes it clear that it is far from a certainty that COVID-19 actually originated at this stall. Only a few stalls were swabbed for SARS-CoV-2 before the market was shut down, and a sample from a freezer at a second stall also tested positive. Samples were also taken from an offsite warehouse which supplied the second stall with animals, and a few of these swabs tested positive as well. Genetic tests on these swabs indicate that the stall sold Amur hedgehogs and Chinese hares. However—and before we get further—it should noted that it is possible that all of these samples tested positive because humans infected with SARS-CoV-2 were shedding the virus at the market and warehouse, not because the wildlife being sold was infected with SARS-CoV-2.

Which stall was more likely to have been the origin of COVID-19? The evidence points to the first stall. 17 drains at Huanan Market were swabbed for SARS-CoV-2, and of those, only three came back positive—including the drain directly in front of the first stall. The other two drains which tested positive were not directly in front of this stall, but were downstream of it and received runoff. Drains associated with the second stall did not return any positive tests.

Which animal did COVID-19 originate from?

The Cell paper identifies a problem—the closest known viral relative of SARS-CoV-2 is a bat coronavirus known as RaTG13 (96.2% sequence similarity), but no bat DNA was found in any of the samples from the Huanan Market. This indicates that there must have been an intermediate host before SARS-CoV-2 made the leap to humans. Masked palm civets might seem to be the obvious culprit, but remarkably, and despite their known susceptibility to SARS-CoV-1, the susceptibility of masked palm civets to SARS-CoV-2 is unknown. Only one other species has been found to carry a coronavirus with >90% similarity to SARS-CoV-2—the pangolin—but no pangolin DNA was found in samples from the Huanan Market. The animal was not sold there. Note that SARS-CoV-2 is only 79.6% similar to SARS-CoV-1. Source

Complicating this issue further is the very strong evidence that SARS-CoV-2 jumped from animals to humans multiple times in 2019. Scientific papers divide the early strains of SARS-CoV-2 in humans into lineage A and lineage B, with lineage A being more closely-related to bat coronaviruses. Bizarrely, lineage A did not appear in Wuhan, China until a week after Lineage B did, even though the closer sequence similarity of lineage A to bat coronaviruses implies that it should have appeared first. Indeed, a landmark study published in the journal Science shows that the most recent common ancestor of lineages A and B evolved in wildlife, not in humans, and that lineage B jumped to humans first, followed shortly thereafter by lineage A. This adds a wrinkle to the problem: it is possible that multiple species were responsible for the origin of COVID-19, and the Science paper also notes that it is likely that there were more than two separate introductions to humans. There may have been as many as 23 animal-to-human introductions in 2019, though this number is highly speculative.

"...the COVID-19 virus was the result of a lab leak."

To be continued in Part 2. Thank you for reading.

(X-post from r/nonmurdermysteries)