[voldacar]

Consider the following scenarios from a Bayesian perspective:

- an outbreak of a novel virus occurs in a city

- an outbreak of a novel virus occurs in a city with a virus lab

- an outbreak of a novel coronavirus occurs in a city with a virus lab that studies coronaviruses

- an outbreak of a novel coronavirus occurs in a city with a virus lab that studies coronaviruses under BSL-3 and BSL-2 conditions

- an outbreak of a novel coronavirus that is genetically similar to RaTG13 occurs in a city with a virus lab that studies coronaviruses under BSL-3 and BSL-2 conditions and contains samples of RaTG13

- an outbreak of a novel coronavirus that is genetically similar to RaTG13 occurs in a city with a virus lab that studies coronaviruses under BSL-3 and BSL-2 conditions and contains samples of RaTG13 and conducts gain of function research on coronaviruses collected from the wild

- an outbreak of a novel coronavirus that is genetically similar to RaTG13 and infects humans through the ACE2 receptor occurs in a city with a virus lab that studies coronaviruses under BSL-3 and BSL-2 conditions and contains samples of RaTG13 and conducts gain of function research on coronaviruses collected from the wild, with the goal of creating viruses that can infect human cells through the ACE2 receptor

- an outbreak of a novel coronavirus that is genetically similar to RaTG13 and infects humans through the ACE2 receptor and has a furin cleavage site (not present in RaTG13, SARS, or other similar coronaviruses) occurs in a city with a virus lab that studies coronaviruses under BSL-3 and BSL-2 conditions and contains samples of RaTG13 and conducts gain of function research on coronaviruses collected from the wild, with the goal of creating viruses that can infect human cells through the ACE2 receptor, and is funded by a group (EcoHealth) which has filed grant applications for research that attempts to insert furin cleavage sites into SARS-like bat coronaviruses

- an outbreak of a novel coronavirus that is genetically similar to RaTG13 and infects humans through the ACE2 receptor and has a furin cleavage site (not present in RaTG13, SARS, or other similar coronaviruses) occurs in a city with a virus lab that studies coronaviruses under BSL-3 and BSL-2 conditions and contains samples of RaTG13 and conducts gain of function research on coronaviruses collected from the wild, with the goal of creating viruses that can infect human cells through the ACE2 receptor, and is funded by a group (EcoHealth) which has filed grant applications for research that attempts to insert furin cleavage sites into SARS-like bat coronaviruses, and multiple years later no animal reservoir of this novel coronavirus has been found, despite the massive incentives for this. In fact they seemingly haven't even been able to fake it by infecting some wild animals deliberately and claiming that they found the zoonotic origin.

I could go on and on but I think you get my point

[a_shovel]

From a Bayesian perspective, it's difficult-to-impossible to evaluate the probability of these events without in-depth knowledge of genetics and/or epidemiology, and they could easily be highly correlated.

The alternative explanation to the lab leak is that the lab was studying factors like infection through ACE2 and furin cleavage sites because they were things considered likely to happen on their own, and were worth preparing for. Studying and preparing for possible mutations is what gain-of-function research is for.

Also, half of the bullets sound like filler. "An outbreak of a novel virus occurs in a city" is definitely filler, and I'd estimate that P( "outbreak of a novel coronavirus occurs in a city with a virus lab that studies coronaviruses" | "an outbreak of a novel virus occurs in a city with a virus lab" ) is probably not that far from 1.00.

And at the end you seem to be proposing the fact that they haven't faked a zoonotic origin is evidence that it was lab-created? That sounds backwards.

When faced with sourceless, pointless suffering, there's not much else to do than clean up the mess and prepare for if it comes back. A person or group of people to blame gives them someone to direct their anger at. If there's a villain, then it's possible to get revenge. People are motivated to create and believe explanations that give them someone to blame, so such explanations deserve more skepticism than others.

The creeping escalation is fun and dramatic, but here it's mainly serving to puff up the amount of evidence at hand.

[voldacar]

> And at the end you seem to be proposing the fact that they haven't faked a zoonotic origin is evidence that it was lab-created? That sounds backwards.

You actually sort of can make that argument, yeah.

At this point, with the lab leak theory having become a lot more popular over the past year or so, the Chinese government would kill to be able to point to an animal reservoir. If they can't find it, the incentive for them to try to fake it is huge. My initial assumption is that if they haven't faked a zoonotic origin, it's probably because they can't, not because they don't want to. By assuming this, I'm assuming that they have basically looked in all the places possible by now, which seems reasonable because they have a lot of manpower and we're 2+ years into the pandemic. If they can't get the virus to infect bats/pangolins/etc, that indicates that the virus didn't originate in the wild and hence supports the lab leak theory

[DiogenesKynikos]

The virus can infect pangolins, bats, and dozens of other mammalian species. It's an incredibly generalist species.

When the outbreak began, China immediately culled virtually all the stock at wild animal farms throughout the country. That is where they thought the virus came from, and they wanted to prevent any more spillover events. One side-effect of that decision is that the animals that most likely served as the intermediate hosts are gone.

With the original SARS in 2002-2003, it was much easier to find the wild animal farms that hosted the virus because the Chinese government did not quickly move to shut them down. The farms remained open for a long time, and there were repeated spillover events.

My guess is that the first reaction of government officials this time around was to just cull all the animals and eliminate the danger right away, and that tracing the origins of the virus wasn't on their minds at that moment.

[jpeloquin]

Sure. P(lab leak origin | last bullet) = P(last bullet | lab leak) * P(lab leak) / P(last bullet). There isn't much evidence to constrain each term, and your post doesn't make any attempt to estimate them, but let's make some stuff up. The values change a lot if you take P(lab leak) to be any lab leak, or specifically a modified RaTG13 from WIV.

Let's go with the more specific scenario. Then P(last bullet | WIV lab leak scenario) becomes P(outbreak | WIV lab leak &c.) because we've conditioned on everything but the outbreak part. I'll guess this is 0.001, which is generous because it's very unlikely for a mere exposure to turn into a pandemic. Exposures to natural potentially pandemic viruses happen every day, most don't become a pandemic. P(WIV lab leak scenario) is difficult. There are a lot of different lab leak scenarios that could have happened instead, but we also don't care that much about trivial differences. Let's be really generous and say P(WIV lab leak scenario) = 0.25 because it's one of I think 4 plausible covid origin sites in Wuhan. Probably it should be lower because it's plausible that Wuhan was only the site of the first superspreader event, not the origin. And let's say P(outbreak) = 0.2 because we seem to get a potential pandemic every 5 years or so. Then P(WIV origin | outbreak) = 0.00125.

There are all sorts of problems with my analysis of course. Even if I haven't made any mistakes, the numbers I conjured up are entirely unconvincing. With only one datum, we have hardly any objective support for our probability estimates, and Bayesian analysis only gives a semblance of objectivity to our prior opinions.

Edit: I have no desire to support either side here, just to point out that probabilistic reasoning doesn't help much here. Whatever happened, happened, regardless of how (un)likely it was.

[voldacar]

I had a longer response but my browser crashed so I'll just try to summarize my thoughts. Our disagreement basically comes down to how we assign priors. I'm not really sure how productive a debate on priors can be because it's not like there are a bunch of previous similar scenarios that we can study in detail.

On P(WIV leak):

Wikipedia[0] lists 50 lab leaks (or more precisely, failure of lab biosecurity measures) in the past century. The actual number is probably much higher because people and institutions like to hide their mistakes. So the base probability of a lab leak happening from a lab that studies pathogens is only moderately low to begin with.

But P(WIV leak) is probably significantly higher than average here, because WIV had worse than average safety procedure.

- According to leaked cables from 2018, american officials & scientists were already concerned about unsafe practices & lack of properly trained personnel at WIV[1]

- WIV researchers collected unknown viruses from bat caves with only hazmat suits + surgical mask as PPE, and handled vials of viral vector specimens without even masks[2]. If they demonstrated poor attention to safety outside the lab, it is likely that they disregarded it within the lab as well

- I recall reading something similar involving Shi Zhengli but I can't find the link now

- Shi Zhengli admitted (!) that bat coronavirus research was performed under BSL-2 and BSL-3 conditions, both of which are significantly more lax than BSL-4[3]

On P(last bullet):

It's a pretty specific scenario, so this probability is very low. It's specific in a way that's meaningful and relevant though, it's not like the specificity came from extraneous things like "and the virus' genome is between 29 and 30 kb" or "and the outbreak occured in a city whose name starts with W".

On P(last bullet | WIV leak):

This probability is essentially a function of the infectiousness of the viruses in the WIV.

> it's very unlikely for a mere exposure to turn into a pandemic. Exposures to natural potentially pandemic viruses happen every day, most don't become a pandemic.

Strongly disagree. The viruses in WIV were deliberately altered, via either natural selection in host cells or direct genetic manipulation, to be significantly more infectious in human cells than a random virus found in the wild would be. It is unlikely for human exposure to a random new virus to lead to a pandemic. That is not the case for human exposure to a new virus that has been altered to be much more competent at infecting humans. Especially considering that these viruses we're talking about are coronaviruses, which are already significantly more infectious than the average virus. SARS2 also has features that are the sort of features we might expect from a virus in the WIV, such as the furin cleavage site and competence at infecting cells through ACE2. WIV research definitely focused on the latter and possibly on the former, so this attribute of the outbreak also increases P(last bullet | WIV leak).

There is also one known precedent for (some pandemic outbreak | some lab leak) which is the 1977 H1N1 flu epidemic. It isn't known with certainty to be from a lab but there is a general consensus that it probably is.[4]

Sorry for not providing numerical estimates for any of these. That would feel super handwavy and they would be, like you admit, entirely unconvincing. Besides, any motivated person can adjust his priors until Bayes spits out the desired outcome. In any case, I feel that the WIV leak theory is simply a more parsimonious explanation of the particular attributes of this pandemic than the zoonotic origin theory. However I doubt there will ever be a "smoking gun" for either theory.

[0] https://en.wikipedia.org/wiki/List_of_laboratory_biosecurity...

[1] https://www.washingtonpost.com/opinions/2020/04/14/state-dep...

[2] https://www.youtube.com/watch?v=ovnUyTRMERI

[3] https://web.archive.org/web/20201206204844/https://www.scien...

[4] https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4542197/

[Symmetry]

For exposures not turning into pandemics, I think it's also important to note that most bat/human coronavirus crossovers occur in relatively small communities that limit the size of potential super spreader events. In something like the original form of Covid-19 where most people infected don't infect anyone else and the small number of people who infect hundreds are the main driver of the high R we can't necessarily generalize from what we see in rural Yunan and SE Asia to what we'd see in a big city. Though regardless of the origins of Covid-19 I do worry about these regions getting more connected to the global economy.

[jpeloquin]

Thanks for your reply. Not providing numerical estimates is fine with me, my opinion is that they're not productive anyway. It's like the Drake equation but worse, or trying to estimate the probability of divine creation vs. a natural origin for the universe. Too many unknowns, no ability to test counterfactuals. We are not even close to inventorying all relevant natural coronaviruses, so we don't have a good estimate for the number of "draws" to assume against the natural origin, and we don't do the routine monitoring that would allow a good estimate of probability for potentially pandemic pathogen → actual pandemic. So an armchair analyst ends up with a solid "maybe", with massive uncertainty intervals, for any explanation.

I completely agree that WIV's practices were dangerous and irresponsible, and that they are a plausible origin at all is a crushing condemnation. There's an old piece of advice: imagine that what you're doing ends up on the front page of the newspaper, and consider whether you would be proud or ashamed. If the latter, do something else. WIV clearly didn't follow that advice.

The facts in your post are all correct to my knowledge, I only quibble with the emphasis on infectiousness. The uniquely dangerous aspect of SARS-CoV-2 was its several-day period of transmissibility in the absence of symptoms, not its infectiousness, which for early strains was not that remarkable. Without asymptomatic transmission it would probably have been contained and quickly forgotten, like SARS-CoV-1. We need to adopt methods that will detect and contain viruses like SARS-CoV-2 so we're better prepared for when SARS-CoV-3 shows up.

[toomim]

This comment is so good that I'm replying to it just so that it appears in my /comments history.

[ricksunny]

Someone had put together an additive Bayesian estimator for origins study.

https://www.getguesstimate.com/models/18631

It’s rudimentary but demonstrates quantitatively how probabilities favoring one origin scenario or another can be reached. Easy to copy-paste it so any set of priors can be applied and collectively estimated,

More rigorous treatment can be found at https://www.researchgate.net/publication/345753939_Outlines_...

There are other similar types of analyses out there if you google around.

[jazzyjackson]

If you click the time code (“one day ago”) to get the comment on its own page, you should see a “favorite” hyperlink, this will add the comment to a list of your favorites, the link to which is at the bottom of your own profile page. Took me a few years of HN to notice it.

[voldacar]

I am honored!

[DiogenesKynikos]

RaTG13 is not the ancestor of SARS-CoV-2. Full stop.

Other, more closely related viruses have recently been found in nature (by a French team in Laos). That immediately 100% rules out all the conspiracy theories that have to do with RaTG13.

I'll also just mention that Wuhan happens to have wet markets where wild animals were sold until the end of 2019. The initial outbreak was clustered around a market that is known to have sold wild animals that are susceptible to SARS-CoV-2. That market is on the opposite side of the city (and it's a big city, about the size of NY) from the WIV.

[relaxing]

Now do a good faith attempt at the same exercise for the natural origin hypothesis.

[Symmetry]

Well, Wuhan is a big transportation hub so regardless of the original crossover point it isn't crazy that the first super-spreader event might happen there.

[OrvalWintermute]

Going to add one, as a proponent for the lab-leak

- an outbreak of a novel coronavirus occurs where the closet natural resivoir sharing a similar bat virus population is between 800 miles (Yunnan province) or > 1000 miles (Laos)

[voldacar]

I didn't add that because I don't think it's really all that compelling. People and biomass get moved around all the time. I don't think the geographical distance really affects the probability by much.

[snapcaster]

Thanks for this comment