8 ms·

The proximal origin of SARS-CoV-2

64 points by KarlKemp 7y ago

Gh0stRAT 7y ago
>While the analyses above suggest that SARS-CoV-2 may bind human ACE2 with high affinity, computational analyses predict that the interaction is not ideal and that the RBD sequence is different from those shown in SARS-CoV to be optimal for receptor binding Sounds like it could evolve to be more transmissible in humans. The more people it infects, the more likely that is to happen. With that in mind, "flattening the curve" is even more essential.
- djsumdog 7y ago
  Most viruses will start very harmful but tend to mutate into less lethal stains causing them to spread further. The Oxford study talks about the S and L strains. The L strain is the more deadly one, but it's likely not made it very far.
  - zbjornson 7y ago
    Source on the first claim? The S/L strain study has been heavily challenged, see commentary at https://nextstrain.org/help/coronavirus/FAQ#is-one-strain-of-the-covid-19-virus-more-severe https://nextstrain.org/help/coronavirus/FAQ#is-one-strain-of...
    - KarlKemp 7y ago
      I do remember this phenomenon being mentioned quite a few times in my genetics classes. Don’t remember the name, unfortunately. But the logic is fairly obvious:a virus wants you to die just as little as humans want the earth to die. As I remember it, it probably wouldn’t make much of a difference here. The classic case mentioned were extremely fast & lethal viruses such as Ebola & Marburg: When a virus kills you within two or three days of infection, any small change can easily double that time and thereby gain significantly better chances of transmission. But for Covid (and, before that, HIV) the infectious period is pretty long already and any improvements would matter less in relative terms.
      - zbjornson 7y ago
        Pathogens can definitely evolve to improve fitness and settle into an ecological balance with their hosts. I more meant to contest that most start out very harmful. I don't think we have data to support that, or to be able to separate virus vs. host adaptations that would cause the appearance of lessened severity, given that most viruses circulating today have ancient origins.
deleted 7y ago
[deleted]
klevertree 7y ago
To summarize, this paper's argument is that SARS-COV-2 can't be lab grown because: 1. It uses a different method of binding to ACE 2 than has previously been found to be most efficient 2. It has several mutations that are of unknown consequence 3. It doesn't have any retrovirus (tool for manipulating virus) backbone The paper then concludes that SARS-COV-2 must be a result of natural selection. While I think this is possible, they ignore the possibility that the virus is a result of artificial selection. If a laboratory were studying how SARS-COV-2 could pass to humans, they might serially pass the virus between mammals (like pangolins) in order to artificially select for mutations. That is, in fact, exactly what previous scientists did in a 2012 experiment with bird flu. They wanted to make it transmissible between mammals, so they serially passed genetically modified bird flu between ferrets until it was. I wrote this up on my blog:https://get21stnight.com/2020/04/14/why-do-some-viruses-cross-over-from-animals/ https://get21stnight.com/2020/04/14/why-do-some-viruses-cros... . The result of this is that bird flu acquired previously unknown mutations in order to pass between mammals. I'm not saying this is what happened, and there are some key differences (i.e. in the bird flu experiment, scientists had to start off with a genetically modified virus). Still, I disagree that we can definitively conclude this was a result of natural selection.
- jostmey 7y ago
  Yes, this virus definitely could be the result of artificial selection, negating the whole argument of this nature medicine paper. That said, I agree that the virus likely emerged as a natural phenomena. Both SARS and MERS emerged as natural phenomena, so there's no reason to believe that SARS-Cov-2 is unnatural.
  - matthewdgreen 7y ago
    I don't think they negate it. They state that it is unlikely, and then they note that the debate is not settled: "More scientific data could swing the balance of evidence to favor one hypothesis over another. Obtaining related viral sequences from animal sources would be the most definitive way of revealing viral origins. For example, a future observation of an intermediate or fully formed polybasic cleavage site in a SARS-CoV-2-like virus from animals would lend even further support to the natural-selection hypotheses."
yokaze 7y ago
Only four dupes ranging from a month ago: https://hn.algolia.com/?q=proximal+origin https://hn.algolia.com/?q=proximal+origin
magwa101 7y ago
Who can believe what is coming out of China?
- KarlKemp 7y ago
  This is an analysis of the viral genome. The only thing that “came out of China” here is the virus itself.
magwa101 7y ago
See this Aussie news program showing the the lockdown in Wuhan. Clearly the authorities were terrified. https://www.youtube.com/watch?v=ycrqXJYf1SU https://www.youtube.com/watch?v=ycrqXJYf1SU
empath75 7y ago
I'm fairly convinced it wasn't designed or engineered, but I do think it escaped from the Wuhan virus lab. That they had invited american scientists to the lab and asked for advice in securing it satisfies me that they weren't doing biological weapons research, the fact that they were studying coronaviruses in a facility where the outbreak happened and americans were sounding the alarm on security months before hand is too much of a coincidence for me to believe the story that it came from a wet market.
- baja_blast 7y ago
  I agree, they were most likely studying SARS like viruses to prevent future outbreaks, but due to employee negligence it got out.
  - abacadaba 7y ago
    I'm torn between not being able to entirely dismiss this theory, and the harm it could cause putting this out there whether true or not. Even more geopolitical distrust is the last thing we need right now, but how do you look the other way? Edit: look the other way referring specifically to any cover up done, fwiw.
    - JoeAltmaier 7y ago
      Its gossip. Don't spread gossip.
      - abacadaba 7y ago
        Welp, cats outta the bag on that one.
        JoeAltmaier 7y ago
        The OP indicated natural origin. The rest is speculation/gossip.
hubadu 7y ago
Why is this one-month-old paper reposted now that the lab leak theory is regaining traction in media outlets? Here is the conclusion of the paper: “[…] we do not believe that any type of laboratory-based scenario is plausible”. Here is the title of Scripps Research Institute press release about their publication: “The COVID-19 coronavirus epidemic has a natural origin, scientists say”. Here are some links to Scripps Research press releases of multi-million dollars deals with chinese labs: https://www.scripps.edu/news-and-events/press-room/2017/20170608chempharma.html https://www.scripps.edu/news-and-events/press-room/2017/2017... https://www.scripps.edu/news-and-events/press-room/2019/20191127-szbl-collaboration.html https://www.scripps.edu/news-and-events/press-room/2019/2019... https://www.biospace.com/article/releases/yisheng-biopharma-announces-research-collaboration-with-the-scripps-research-institute-in-developing-new-aids-vaccine-/ https://www.biospace.com/article/releases/yisheng-biopharma-... I am not going to address the china-praising statements and political stances from main researcher twitter account at a time when CCP cover-up was already known worldwide. At the time this paper was published, moderators on social networks deleted any possible discussion on the topic. Copy-paste op's link in reddit search bar and see how many comments were deleted from related discussion.
- Aperocky 7y ago
  Are you suggesting that .. China is going to engineer a virus and release it in its own population? And then shut the whole country down and pray that it would spread fast and worse elsewhere? Let's just say that back in early February nobody even in China thought that other countries are going to be affected. It is a disaster for the CCP at the time that had popular opinion on the internet swing suddenly and violently against the government. Now, seeing how other countries reacted, that suddenly was not the case anymore. And the CCP have no ability to control other countries action.
  - empath75 7y ago
    The theory that it escaped from the lab does not imply that it was engineered -- they could very well have been doing legitimate medical research and made a mistake.
  - 7y ago

64 points by KarlKemp 7y ago

>While the analyses above suggest that SARS-CoV-2 may bind human ACE2 with high affinity, computational analyses predict that the interaction is not ideal and that the RBD sequence is different from those shown in SARS-CoV to be optimal for receptor binding Sounds like it could evolve to be more transmissible in humans. The more people it infects, the more likely that is to happen. With that in mind, "flattening the curve" is even more essential.

djsumdog 7y ago
Most viruses will start very harmful but tend to mutate into less lethal stains causing them to spread further. The Oxford study talks about the S and L strains. The L strain is the more deadly one, but it's likely not made it very far.
- zbjornson 7y ago
  Source on the first claim? The S/L strain study has been heavily challenged, see commentary at https://nextstrain.org/help/coronavirus/FAQ#is-one-strain-of-the-covid-19-virus-more-severe https://nextstrain.org/help/coronavirus/FAQ#is-one-strain-of...
  - KarlKemp 7y ago
    I do remember this phenomenon being mentioned quite a few times in my genetics classes. Don’t remember the name, unfortunately. But the logic is fairly obvious:a virus wants you to die just as little as humans want the earth to die. As I remember it, it probably wouldn’t make much of a difference here. The classic case mentioned were extremely fast & lethal viruses such as Ebola & Marburg: When a virus kills you within two or three days of infection, any small change can easily double that time and thereby gain significantly better chances of transmission. But for Covid (and, before that, HIV) the infectious period is pretty long already and any improvements would matter less in relative terms.
    - zbjornson 7y ago
      Pathogens can definitely evolve to improve fitness and settle into an ecological balance with their hosts. I more meant to contest that most start out very harmful. I don't think we have data to support that, or to be able to separate virus vs. host adaptations that would cause the appearance of lessened severity, given that most viruses circulating today have ancient origins.

deleted 7y ago

[deleted]

klevertree 7y ago

To summarize, this paper's argument is that SARS-COV-2 can't be lab grown because: 1. It uses a different method of binding to ACE 2 than has previously been found to be most efficient 2. It has several mutations that are of unknown consequence 3. It doesn't have any retrovirus (tool for manipulating virus) backbone The paper then concludes that SARS-COV-2 must be a result of natural selection. While I think this is possible, they ignore the possibility that the virus is a result of artificial selection. If a laboratory were studying how SARS-COV-2 could pass to humans, they might serially pass the virus between mammals (like pangolins) in order to artificially select for mutations. That is, in fact, exactly what previous scientists did in a 2012 experiment with bird flu. They wanted to make it transmissible between mammals, so they serially passed genetically modified bird flu between ferrets until it was. I wrote this up on my blog:https://get21stnight.com/2020/04/14/why-do-some-viruses-cross-over-from-animals/ https://get21stnight.com/2020/04/14/why-do-some-viruses-cros... . The result of this is that bird flu acquired previously unknown mutations in order to pass between mammals. I'm not saying this is what happened, and there are some key differences (i.e. in the bird flu experiment, scientists had to start off with a genetically modified virus). Still, I disagree that we can definitively conclude this was a result of natural selection.

jostmey 7y ago
Yes, this virus definitely could be the result of artificial selection, negating the whole argument of this nature medicine paper. That said, I agree that the virus likely emerged as a natural phenomena. Both SARS and MERS emerged as natural phenomena, so there's no reason to believe that SARS-Cov-2 is unnatural.
- matthewdgreen 7y ago
  I don't think they negate it. They state that it is unlikely, and then they note that the debate is not settled: "More scientific data could swing the balance of evidence to favor one hypothesis over another. Obtaining related viral sequences from animal sources would be the most definitive way of revealing viral origins. For example, a future observation of an intermediate or fully formed polybasic cleavage site in a SARS-CoV-2-like virus from animals would lend even further support to the natural-selection hypotheses."

yokaze 7y ago

Only four dupes ranging from a month ago: https://hn.algolia.com/?q=proximal+origin https://hn.algolia.com/?q=proximal+origin

magwa101 7y ago

Who can believe what is coming out of China?

KarlKemp 7y ago
This is an analysis of the viral genome. The only thing that “came out of China” here is the virus itself.

magwa101 7y ago

See this Aussie news program showing the the lockdown in Wuhan. Clearly the authorities were terrified. https://www.youtube.com/watch?v=ycrqXJYf1SU https://www.youtube.com/watch?v=ycrqXJYf1SU

empath75 7y ago

I'm fairly convinced it wasn't designed or engineered, but I do think it escaped from the Wuhan virus lab. That they had invited american scientists to the lab and asked for advice in securing it satisfies me that they weren't doing biological weapons research, the fact that they were studying coronaviruses in a facility where the outbreak happened and americans were sounding the alarm on security months before hand is too much of a coincidence for me to believe the story that it came from a wet market.

baja_blast 7y ago
I agree, they were most likely studying SARS like viruses to prevent future outbreaks, but due to employee negligence it got out.
- abacadaba 7y ago
  I'm torn between not being able to entirely dismiss this theory, and the harm it could cause putting this out there whether true or not. Even more geopolitical distrust is the last thing we need right now, but how do you look the other way? Edit: look the other way referring specifically to any cover up done, fwiw.
  - JoeAltmaier 7y ago
    Its gossip. Don't spread gossip.
    - abacadaba 7y ago
      Welp, cats outta the bag on that one.
      - JoeAltmaier 7y ago
        The OP indicated natural origin. The rest is speculation/gossip.

hubadu 7y ago

Why is this one-month-old paper reposted now that the lab leak theory is regaining traction in media outlets? Here is the conclusion of the paper: “[…] we do not believe that any type of laboratory-based scenario is plausible”. Here is the title of Scripps Research Institute press release about their publication: “The COVID-19 coronavirus epidemic has a natural origin, scientists say”. Here are some links to Scripps Research press releases of multi-million dollars deals with chinese labs: https://www.scripps.edu/news-and-events/press-room/2017/20170608chempharma.html https://www.scripps.edu/news-and-events/press-room/2017/2017... https://www.scripps.edu/news-and-events/press-room/2019/20191127-szbl-collaboration.html https://www.scripps.edu/news-and-events/press-room/2019/2019... https://www.biospace.com/article/releases/yisheng-biopharma-announces-research-collaboration-with-the-scripps-research-institute-in-developing-new-aids-vaccine-/ https://www.biospace.com/article/releases/yisheng-biopharma-... I am not going to address the china-praising statements and political stances from main researcher twitter account at a time when CCP cover-up was already known worldwide. At the time this paper was published, moderators on social networks deleted any possible discussion on the topic. Copy-paste op's link in reddit search bar and see how many comments were deleted from related discussion.

Aperocky 7y ago
Are you suggesting that .. China is going to engineer a virus and release it in its own population? And then shut the whole country down and pray that it would spread fast and worse elsewhere? Let's just say that back in early February nobody even in China thought that other countries are going to be affected. It is a disaster for the CCP at the time that had popular opinion on the internet swing suddenly and violently against the government. Now, seeing how other countries reacted, that suddenly was not the case anymore. And the CCP have no ability to control other countries action.
- empath75 7y ago
  The theory that it escaped from the lab does not imply that it was engineered -- they could very well have been doing legitimate medical research and made a mistake.
- 7y ago