We in fact have a standard method to test whether sequence is under selection or not, and engineering is a kind of selection. It is called Ka/Ks ratio.
For SARS-CoV-2, there were 79 amino acid changes and 475 silent changes relative to known common ancestor. This is a strong signature of purifying selection, hence against any engineering. The article does not address this evidence at all.
You can argue that sequence was engineered specifically so that it doesn't look engineered. That's impossible to refute with sequence evidence, but also not compatible with accidental release.
I did it myself in the first days that the sequence was available and came to the same conclusion that this is almost certainly natural in origin and it helps to point out that bats are the most genetically diverse among mammals representing around 1 in 5 mammal species. There aren't that many bat genome sequences that have been performed and so it isn't completely unexpected to find that the spike protein has recombined with a sequence that isn't known. You can however do the translation to amino acid sequence and then search just that spike sequence against known proteins in NCBI and find that it is quite close on the protein level to other known bat proteins, at least in part.
I don't think it is engineered, however it still could be a strain that was collected and analyzed at the Wuhan lab. I don't know if we will ever have the full story on that possibility.
> however it still could be a strain that was collected and analyzed at the Wuhan lab. I don't know if we will ever have the full story on that possibility.
Exactly. It's possible. Who knows if we'll ever know.
The only thing that bothers me about this whole story is the multitudes suggesting an accidental leak is pure "conspiracy theory", when in fact it's a plausible hypothesis.
It is truly puzzling that so many people are so strongly, and so emotionally, opposed to the idea of an accidental leak.
Ah yes, I am familiar with that thread – I've been following it.
One thing does strike me as strange. The common ancestor here, RaTG13, was only sequenced and published by Shi's lab in Wuhan in late January. Despite supposedly being sequenced in 2013. Shi's Wuhan lab is the same one in question in this article regarding a potential leak.
Is this unusual for a lab to do, or is this common practice?
Others have asked this question in the Twitter thread you posted, but no one has responded so far as I can see. E.g:
This is not completely unusual. Maybe they had collected many environmental samples for a project that had not yet been published and decided to release that information to the public because it was a closer relative to COVID19. I personally have sequence data that I'm sitting on prior to publication that was collected 2 years ago and some others that are from around 6 years ago. It isn't completely unusual.
This is fake news. It's kind of repetitive, maybe alarmist. It leans on the idea that the Wuhan virus is HIV-like even after it acknowledges that the paper suggesting the comparison was withdrawn. The blog is about inequality and the prison system, not virology.
On the other hand, here's a reputable news source quoting the head of the international effort to study the genome of the Wuhan virus. He says it's fake news too.
The article doesn't make the claim that everything is 100% correct. It is simply pointing out some interesting problems with the analysis of the virus so far, and also pointing out some events that seem to be more than coincidences.
> And so a scientist who’s been prolifically involved with studying the molecular interaction of coronaviruses and humanity, spending decades and millions of dollars, and having even helped build a hyper-virulent coronavirus from scratch at UNC – just so happens to be working at the only BSL-4 virology lab in China that also just so happens to be at the epicenter of an outbreak involved a coronavirus that’s escaping zoological classification and whose novel spike-protein region shares more in common with a commercial genetic vector than any of its wild relatives, and has other unnatural characteristics that will be discussed below.
We can't "fully" dismiss accidental release idea, but we can pretty much dismiss it, because sequence (we now have sequence from outside of China, it's not under Chinese control) strongly suggests natural and not artificial origin (see my other comment).
If we are to argue "artificial to look like natural", that's premeditated release, not accidental release.
Not sure how plausible it is, but the article does claim the virus's creation could be part of a red-teaming exercise gone wrong, which would be consistent with a naturally-selected genome wouldn't it?
The evidence that it's natural is based on similarities to a common ancestor, RaTG13. Googling "RaTG13" will turn up results suggesting it's natural over artificial.
What is truly bizarre is that the gene sequence of this common ancestor RaTG13 was only released in late January 2020 by Shi's lab in Wuhan – the same lab in question regarding the leak.
For the moment, I am hesitant to trust any research premised on analysis of RaTG13.
First, RaTG13 is not an ancestor, it's a sibling. Next, the evidence is based on ratio of amino acid changes to silent changes, not based on similarity.
Yes – sibling, not ancestor. Regardless, the analysis is premised on the RaTG13 genome, and I am somewhat skeptical of analysis based on RaTG13.
I think accidental release of a naturally evolved virus is still a plausible hypothesis. To discount it as "conspiracy theory" seems to be wishful thinking.
I will continue to monitor findings on this until more conclusive, non-RaTG13 derived evidence is available.
...sequencing, combined with sampling the market’s environment for the presence of the virus, is clarifying that it indeed had an important early role in amplifying the outbreak. The viral sequences, most researchers say, also knock down the idea the pathogen came from a virology institute in Wuhan.
Note that the article is dated more than two weeks ago.
>Beijing has had four known accidental leaks of the SARS virus in recent years, so there is absolutely no reason to assume that this strain of coronavirus from Wuhan didn’t accidentally leak out as well. This is unlikely to be a plot twist in one of the novels Tom Clancy wrote after he started mailing it in.
https://en.wikipedia.org/wiki/Ka/Ks_ratio
For SARS-CoV-2, there were 79 amino acid changes and 475 silent changes relative to known common ancestor. This is a strong signature of purifying selection, hence against any engineering. The article does not address this evidence at all.
You can argue that sequence was engineered specifically so that it doesn't look engineered. That's impossible to refute with sequence evidence, but also not compatible with accidental release.