Bats — aside from the few blood-drinking bats which aren't implicated, and aren't they New-World species anyway — don't tend to interact much with other mammals or with birds. Without human intervention, there's not much opportunity for them to infect humans or any other animals. Carnivores (raptors, felines, to a lesser extent maybe even canines) do eat bats, but not commonly, and they're unlikely to spread disease further due to their lack of social behavior.
Neither bats nor pangolins are factory farmed (it seems some people have tried with pangolins, given their delicacy status, but they're not easy enough to raise in captivity to make it worthwhile). Bush meat and wet markets create other disease risks, but not the concentrated disease reservoir effect you're pointing out as a problem in factory farming, i.e. typically swine or fowl. There are many reasons to reduce factory farming (meat consumption per capita); disease risk is just one of them. Diseases in factory farms can be monitored, particularly these days with cheap DNA/RNA sequencing. Diseases from wild animals sold in wet markets... no surveillance... greater risk.
Given the bats are the most likely original source, and given that Wuhan lab scientists travelled and collected bat virus samples from where those species of bats actually live, the obvious most likely theory is that there was an accidental leak of a natural or derived virus from the WIV (or at least from WIV scientists on return from one of their trips if you cling to the theory that SARS-CoV-2 is of entirely natural origin).
This is incorrect.
Bat (Rhinolophus) sarbecoviruses have been isolated and sequenced in Hubei:
https://www.ncbi.nlm.nih.gov/nuccore/DQ648856
https://www.ncbi.nlm.nih.gov/nuccore/DQ648857
The closest KNOWN bat sarbecovirus was found in Yunnan, but it was only 96% identical. That doesn't preclude the actual 98-99% identical progenitor virus of SARS-CoV-2 from living in Hubei.
Rhinolophus bats are all over southern China, and neighboring countries with a very wide range, and the all carry SARS-CoV-like viruses.
Also nothing precludes the species jump from bats to farmed animals happening in Yunnan and then infected animals being transported to farms in Hubei.
I also never mentioned pangolins or wet markets because we know at this point that neither of those are related. The animals to focus on would be minks and other mustelids or raccoon dogs or other farmed animals.
And we already know that SARS-CoV-1 likely originated in bats in Yunnan (where the "WIV1" coronavirus was found) while the leap to humans from an intermediate animal is thought to have happened in Guangdong. Again we have here a problem of "how did the virus in Yunnan jump to people 700+ miles away?" but in the SARS-CoV-1 case there's no weapons laboratory distraction. It happened back then with SARS-CoV-1 so therefore any objections you can have about coronavirus jumping species and geography is just falsified. It is unlikely clearly or this would just happen every other year.
> We have done bat virus surveillance in Hubei Province for many years, but have not found that bats in Wuhan or even the wider Hubei Province carry any coronaviruses that are closely related to SARS-CoV-2. I don't think the spillover from bats to humans occurred in Wuhan or in Hubei Province.
https://www.sciencemag.org/sites/default/files/Shi%20Zhengli...
Anyways, the point isn't that a natural zoonotic jump in Wuhan is perfectly impossible. Even if we assumed (wrongly, at least if you believe Dr. Shi) that natural zoonosis was equally probable in any city in China, the emergence of SARS-CoV-2 in Wuhan is still evidence in favor of a lab accident. To a good first approximation, the WIV does 100% of the research on novel SARS-like viruses in China, so an outbreak due to a lab accident would probably emerge there. So whatever your Bayesian prior was for natural vs. lab accident, its emergence in Wuhan should update that by a factor of ~100 (i.e., the population of China divided by the population of Wuhan).
And I'm not sure why you think farmed animals are likely intermediate hosts? China has been sampling extensively, and while it's not necessarily easy to find the intermediate host (e.g., for Ebola), that should be far easier in a factory farm than in the wilderness. So why haven't they found that?
Finally, I don't think anyone brought up weapons here except you? That seems like a deliberate conflation, introducing outlandish theories for which no evidence exists ("SARS-CoV-2 was designed as a bioweapon") to discredit the more likely theory actually being discussed ("SARS-CoV-2 originated from a lab accident during internationally-funded basic research").
And again there's the SARS-CoV-1 where bat viruses in Yunnan jumped to people in Guangdong, 700+ miles away. And you'd have to look at the whole population around Wuhan where it is the closest major city (and Wuhan itself is the largest major city in central China, which makes it comparable to massive cities like NYC).
The probability is likely closer to 10%, and SARS-CoV-1 already lost that die roll and wound up in Guangdong. This time you rolled and got a 10% result. That isn't very unsurprising. Your p value is not significant.
And, yeah, I don't think that they've done everything they can to survey broadly. The studies that they've done tend to collect a bunch of bats from a particular cave and sequence the viruses in them and then draw broad conclusions about the whole province. There's only two sarbecoviruses sequences they've found in Hubei. I'd be much more comfortable with statements that SARS-CoV-2-like sarbecoviruses aren't found in Hubei if they'd sequenced 100 of them.
EDIT: Yeah so Wuhan is 6% of the population of all cities in China of roughly its size. But Shanghai is father away so its 24M should be weighted less, so with Tianjin and Nanjing. Beijing is way further away and its weighting should be fairly negligible. Chengdu and Chongqing are slightly closer. Of the top 10 Guangzhou and Shenzhen are both similarly close and in Guangdong where the SARS-CoV-1 spillover happened. My 10% gut estimate still looks pretty good -- "pick a random top 20 city in China somewhat near Yunnan where the bats are" and Wuhan is not that improbable at all.
As to specific numbers, 10% seems too low to me--Wuhan is 6% of the population of Chinese cities at least as big as Wuhan, disregarding smaller cities entirely, including Foshan where the original SARS emerged, and disregarding Dr. Shi's expectation that origin closer to Yunnan was more likely. But at least we're within an order of magnitude of each other.
Knowing nothing whatsoever except that a pandemic emerged, what's your prior for lab vs. natural origin? It depends how you count, but we've had perhaps a dozen pandemics in the last fifty years, and one (the 1977 flu) was near-certainly lab-origin. So even with extreme optimism as to lab safety improvements, I can't see how you'd estimate less than e.g. 1%. For SARS-CoV-2, you'd perhaps adjust down for the novelty of the pathogen (since most lab work is with known pathogens--though most of the WIV's seems not to have been). It doesn't take that many p = 10% coincidences up to get to even odds or better, though.