The origin of Covid: Did people or nature open Pandora’s box?

When China was quenching their epidemic whole wester world was going "omg, look at those totalitarian, weak dumbasses, pass me the popcorn"

Nicholas has Waded (pun intended) into the waters of irrational horror over gain-of-function research that seems to gain viral traction following every spill-over event. The only argument presented in the article that leans towards the lab-leak hypothesis is the human-preffered double CGG codon that appears in the furin cleavage site; this is nothing like a smoking gun, IMO. Yesterday's TWiV 751 covered a paper The furin cleavage site in the SARS-CoV-2 spike protein is required for transmission in ferrets [1] which has the following abstract:

> To investigate the importance of the spike polybasic CS of SARS-CoV-2 (PRRAR), a number of spike mutants predicted to modulate the efficiency of furin cleavage were generated (Fig. 1a), including: substituting two upstream arginines to produce a monobasic CS similar to SARS-CoV spike (monoCS), replacing the tribasic CS with the furin CS of a highly pathogenic H5N1 avian influenza haemagglutinin containing seven basic amino acids (H5CS) and two naturally occurring deletions seen following passage in Vero E6 cells and/or in clinical isolates21,26. The first deletion removes eight amino acids including all three arginines of the PRRAR site (ΔCS), while the other removes five flanking amino acids but retains the tribasic CS (Δflank). The mutations were engineered into a spike expression plasmid to enable cell surface expression and generation of coronavirus lentiviral PVs. In addition, to study the importance of the PRRAR motif in the context of live virus, we used a naturally occurring Vero-cell-adapted mutant SARS-CoV-2, ΔCS26. This variant and the wild-type (WT) virus from which it was derived were cloned by limiting dilution to enable studies using individual genotypes.

This is the horror of in vitro and in vivo viral lab research and the result is a magnificent advancement of our understanding of SARS-CoV-2, the furin cleavage site, and its role in TMPRSS2 assisted membrane entry. This research follows the equally eye-opening paper covered in TWiV 715 that explained why hydroxychloroquine (HCQ) failed; Vero E6 cells lack TMPRRS2 so HCQ fully blocks entry via endocytosis. It should be noted that this study includes MERS-CoV which also has a furin cleavage site; falsifying one of the claims of Wade's article.

Regardless, lab experiments begin with one or more viral isolates and molecular clock techniques should show that the original Wuhan variant has almost identical non-coding genome segments compared to existing lab isolates. The RaTG13 sequence is a very distant relative using this measure. Also, RaTG13 is not an isolate, only an RNA sample collected in wild bat anal swabs. Conflating viral isolates with RNA samples seems to be a common error; an entry in a genetic database does not imply that a viable viral line exists in a lab. A RaTG13 lab isolate would have been an important achievement to further our scientific understanding.

I'm confused by the dismissals of the natural origins hypothesis. The horseshoe bat roosts, that are studied, are mostly found in or near Kunming, Yunnan. This lush wild area is part of the Lancang/Mekong River watershed/ecosystem shared by nocturnal bats and nocturnal arboreal mammals like palm civets, pangolins, and raccoon dogs. The nearby villages contain people engaged in guano collection, the wildlife trade, and domestic livestock farming.

The average incubation time of COVID-19 is 4.5 days. Armed with Google maps and a basic understanding of planes, trains, and automobiles we can gauge travel time from Kunming Airport to either Wuhan Tianhe International Airport (2 hr 5 min) or Guangzhou Baiyun International Airport (2 hrs). In 2003, SARS-1 emerged in Guangzhou (near Hong Kong) and the now demonized Dr. Zheng-li Shi and her team traced the origins to palm civets (the intermediate host). Why is this so hard? Why do we not ridicule the assumption that travel between major Chinese transportation hubs must leave a wake of infections along the path?

Finally, Wade's article mentions a U.S. State Department claim [2]:

> The U.S. government has reason to believe that several researchers inside the WIV became sick in autumn 2019, before the first identified case of the outbreak, with symptoms consistent with both COVID-19 and common seasonal illnesses.

If true, this is an important early super-spreader event but the remainder of the release consists of a facile analysis performed by people more knowledgeable in geopolitics than science.

[1] https://www.nature.com/articles/s41564-021-00908-w

[2] https://2017-2021.state.gov/fact-sheet-activity-at-the-wuhan...

The species of bats allegedly involved are not near Wuhan.

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).

As claimed by Rogin, the medical research community is privately divided but largely unwilling to speak out publicly because they don’t want to be labeled conspiracy theorists, don’t want to be associated with supporting a position tangentially aligned with trump, and first and foremost don’t want to jeopardize their grants or careers.

According to Rogin, Fauci did not so much covertly direct funds, but rather, quietly reinstated gain a function research which was stopped by the Obama administration (without approval from the Trump administration). He also doubled down with new grants in the same area as a response to the pandemic.

I personally find none of this particularly difficult to believe given other positions the medical establishment has taken over the coarse of the pandemic and the extreme lack of curiosity in the press.

Except that after 15 months of global catastrophy and investigation, no evidence has been found in support of that.

Please correct me if I'm wrong, but it would seem that if 'minks' were the problem, there would be trail of evidence to pick up on.

Hence the notion of speculation / Occam's Razor.