4 ms·

Exploration into the Origins of the Wuhan Strain of Coronavirus (2019-NCoV)

33 points by skmurphy 7y ago

sigmar 7y ago
This is all drivel and extremely irresponsible. >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.
deleted 7y ago
[deleted]
mnemonicsloth 7y ago
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on the idea that the Wuhan virus is HIV-like even after it acknowledges that the paper suggesting the comparison was withdrawn.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. https://www.ft.com/content/a6392ee6-4ec6-11ea-95a0-43d18ec715f5 https://www.ft.com/content/a6392ee6-4ec6-11ea-95a0-43d18ec71...
- s_y_n_t_a_x 7y ago
  I don't see how you can fully dismiss the idea that it was an accidental outbreak from a lab, especially when there's precedent. The truth is we don't know yet, and we can't trust the Communist Party of China. If you have an issue with the article please point out something specific instead of stating innuendos. An expert scientist on coronaviruses that made one from scratch at UNC was working in Wuhan. The virology lab is across the street from the animal market the outbreak originated at. If that's not plausible, what is?
  - mnemonicsloth 7y ago
    I didn't state innuendo. I quoted the leading expert in the world right now saying that the Wuhan virus is not engineered. I don't trust the CPC either, but when the experts speak you have to listen.
    - s_y_n_t_a_x 7y ago
      > I didn't state innuendo. You didn't quote anything from the article. If you have a specific concern with a statement they are using please quote it and state your concern. > I quoted the leading expert in the world right now saying that the Wuhan virus is not engineered. No you linked to a paywall so I was unable to view the quote. If scientists find the origin of the virus we can finally say that it wasn't engineered, currently they have not. You cannot fully dismiss this possibility yet, especially the circumstances and previous lab outbreaks.
      - mnemonicsloth 7y ago
        > If scientists find the origin of the virus we can finally say that it wasn't engineered, currently they have not. No, they have. https://www.sciencemag.org/news/2020/01/mining-coronavirus-genomes-clues-outbreak-s-origins https://www.sciencemag.org/news/2020/01/mining-coronavirus-g... ...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.
        s_y_n_t_a_x 7y ago
        If it out-broke from the virology lab across the street from the market then yes it would have a presence of the market's environment.
  - sanxiyn 7y ago
    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.
- Thorentis 7y ago
  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.
sanxiyn 7y ago
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. https://en.wikipedia.org/wiki/Ka/Ks_ratio 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.
- 12elephant 7y ago
  Where did you see this result?
  - sanxiyn 7y ago
    You can do this yourself, it's a standard bioinformatics exercise. But in fact, I have seen it here: https://twitter.com/trvrb/status/1224207554600792064 https://twitter.com/trvrb/status/1224207554600792064
    - 12elephant 7y ago
      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: https://twitter.com/LizSpecht/status/1223394697948753922 https://twitter.com/LizSpecht/status/1223394697948753922 and https://twitter.com/LizSpecht/status/1223451393173803014 https://twitter.com/LizSpecht/status/1223451393173803014
      - jhart99 7y ago

33 points by skmurphy 7y ago

This is all drivel and extremely irresponsible. >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.

deleted 7y ago

[deleted]

mnemonicsloth 7y ago

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. https://www.ft.com/content/a6392ee6-4ec6-11ea-95a0-43d18ec715f5 https://www.ft.com/content/a6392ee6-4ec6-11ea-95a0-43d18ec71...

s_y_n_t_a_x 7y ago
I don't see how you can fully dismiss the idea that it was an accidental outbreak from a lab, especially when there's precedent. The truth is we don't know yet, and we can't trust the Communist Party of China. If you have an issue with the article please point out something specific instead of stating innuendos. An expert scientist on coronaviruses that made one from scratch at UNC was working in Wuhan. The virology lab is across the street from the animal market the outbreak originated at. If that's not plausible, what is?
- mnemonicsloth 7y ago
  I didn't state innuendo. I quoted the leading expert in the world right now saying that the Wuhan virus is not engineered. I don't trust the CPC either, but when the experts speak you have to listen.
  - s_y_n_t_a_x 7y ago
    > I didn't state innuendo. You didn't quote anything from the article. If you have a specific concern with a statement they are using please quote it and state your concern. > I quoted the leading expert in the world right now saying that the Wuhan virus is not engineered. No you linked to a paywall so I was unable to view the quote. If scientists find the origin of the virus we can finally say that it wasn't engineered, currently they have not. You cannot fully dismiss this possibility yet, especially the circumstances and previous lab outbreaks.
    - mnemonicsloth 7y ago
      > If scientists find the origin of the virus we can finally say that it wasn't engineered, currently they have not. No, they have. https://www.sciencemag.org/news/2020/01/mining-coronavirus-genomes-clues-outbreak-s-origins https://www.sciencemag.org/news/2020/01/mining-coronavirus-g... ...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.
      - s_y_n_t_a_x 7y ago
        If it out-broke from the virology lab across the street from the market then yes it would have a presence of the market's environment.
- sanxiyn 7y ago
  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.
Thorentis 7y ago
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.

sanxiyn 7y ago

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. https://en.wikipedia.org/wiki/Ka/Ks_ratio 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.

12elephant 7y ago
Where did you see this result?
- sanxiyn 7y ago
  You can do this yourself, it's a standard bioinformatics exercise. But in fact, I have seen it here: https://twitter.com/trvrb/status/1224207554600792064 https://twitter.com/trvrb/status/1224207554600792064
  - 12elephant 7y ago
    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: https://twitter.com/LizSpecht/status/1223394697948753922 https://twitter.com/LizSpecht/status/1223394697948753922 and https://twitter.com/LizSpecht/status/1223451393173803014 https://twitter.com/LizSpecht/status/1223451393173803014
    - jhart99 7y ago