The #OriginOfCovid raccoon dog that did not bark

posted: January 6, 2024

tl;dr: If B necessarily follows A, and B is not observed, then we can conclude something about A...

Computers are logic machines, and I’ve based my entire professional career on the mastery of them. If I weren’t adept at logic, I would have had to pursue some other career.

The phrase “the dog that didn’t bark” refers to a Sherlock Holmes story written by Sir Arthur Conan Doyle, “The Adventure of Silver Blaze”. I can’t recall reading the story, but I’ve certainly read about the story. Sherlock Holmes solves the mystery not because of something the dog did, but rather something the dog did not do. No barking was heard while, according to the leading theory of the case at the time, the dog was in the presence of a stranger. Therefore, Holmes reasoned, the stranger could not have been in the dog’s presence, which led Holmes towards a different, and correct, solution.

The “dog that didn’t bark” situation comes up all the time in detective work, debugging computer software, and yes, scientific research. If you cannot directly observe the original event, then you can try to observe its aftereffects. The aftereffects are those events that necessarily follow the original event every time the original event happens. If none of the aftereffects can be observed, then one can reasonably conclude that the original event did not happen. More formally, if event B necessarily follows event A (i.e. A always causes B), and B is not observed after sufficiently searching for it, then one can conclude that event A did not occur.

There’s a “dog that didn’t bark” situation with the leading zoonotic theory for the origin of COVID-19. The Huanan Seafood Wholesale Market in Wuhan theory (Worobey et al, 2022) posits two spillover events in which the virus was transmitted from intermediate host animals to human beings. SARS-1 spilled over from civet cats who were originally infected with a bat virus, so the Huanan market theory proposes that SARS-2 was also due to China’s tolerance of trade in exotic animals.

We know, thanks to SARS-1, what China does when a novel coronavirus spills over from animals to humans and causes an outbreak of a new disease: they find and cull the intermediate host animal to prevent further spillover events. Although some scientists, such as Francis Collins, like to say that it took China fourteen years to find the intermediate host for SARS-1, that is a misleading statement: China was culling civet cats in January 2004, as documented by the Washington Post.

We also know some of the steps that China took after the initial COVID-19 outbreak. They instituted a severe lockdown in Wuhan, the first lockdown in what became a multiyear “Zero COVID” policy to attempt to eradicate the virus from China. They closed the Huanan market on December 31, 2019, and did significant testing in the market. They found many environmental samples that tested positive for the SARS-CoV-2 virus, but no animals tested positive.

A grainy, poorly lit photo of two furry animals in the back of a gray metal cage, with the two eyes of one reflecting light from the camera's flash, with an empty cage and some stacked bins in the background

The intermediate host of SARS-CoV-2, five years before the pandemic started?

Given China’s strict Zero COVID policy and behavior after the SARS-1 outbreak, it’s certainly reasonable to expect that China would have done everything possible to identify the intermediate host of the SARS-CoV-2 virus and cull it to prevent more spillovers. Eradicating the virus requires finding and isolating all human hosts, which China did, and killing the animal hosts. Yet here we are, more than four years after the initial outbreak, and the intermediate host animal remains unidentified. There is no concrete evidence that China did any significant culling. These are the two event Bs that necessarily follow event A, the spillover at the Huanan market. Since the event Bs have not occurred, what should we conclude about event A? How do zoonotic proponents explain the dog that did not bark?

Most of the scientists promoting the Huanan market spillover theory keep proposing various animal species as the intermediate host, including pangolins, raccoon dogs, civet cats, and others. Australian virologist Eddie Holmes, who collaborated with the Wuhan Institute of Virology (WIV), publicized a photo he took of a raccoon dog in the Huanan market in 2014. However, even spillover proponents admit that insufficient evidence exists to say what the intermediate host animal is. So they either fall back on the same statement that Collins made, which is that it might take fourteen years to find the intermediate host, or they say that the intermediate host may never be found. It either vanished without a trace, or so many individual animals have now been infected with SARS-CoV-2 that it is impossible to identify animals with the progenitor version of the virus. They implicitly or explicitly accuse Chinese scientists of incompetence by criticizing China’s inability to detect the virus in the intermediate host in the early days of the outbreak. Spillover proponents are also highly critical of the lack of positive animal tests in the Huanan market tests. They claim that the vendors of the possible intermediate host species were tipped off that the testing would happen, giving them time to remove the infected animals.

That leads into more exotic theories about the lack of evidence of culling, voiced by some scientists and others that I have interacted with on X/Twitter. Some say that removal of infected animals from the Huanan market was because China did not want the world to know that they still tolerated trade in exotic animals - yet the entire world does know this. Some say that China does know the identity of the intermediate host animal and is covering it up. The problem with China deflecting attention from the Huanan market spillover theory is that the lab leak theory draws more attention. The Chinese Communist Party does not want the world’s eyes on WIV, which does work on behalf of the People's Liberation Army.

Hiding a culling program would be difficult. If the intermediate host animal is not known and all possible intermediate hosts need to be culled, it’s even more difficult. The animals sold at the market come from farms and supply chains that necessarily stretch all the way back to where the bat viruses most similar to SARS-CoV-2 are plentiful, which is hundreds of miles away from Wuhan. One person on X/Twitter tried to convince me that China did have a massive, multi-species culling program, and successfully covered it up. Another person, recently, claimed that the Huanan market was a unique environment that had just the right mix of animals in it, such that the virus evolved and appeared only there. Hence no culling was needed and all China needed to do to prevent more spillovers was shut down the Huanan market.

The Huanan market theory has other problems with it, but proponents have an especially tough time explaining the absence of two event Bs, the identification of the intermediate host and evidence of a culling program. Might that allow us to reasonably conclude that event A, the two spillovers at the Huanan market, did not happen?