5 ms·

Standard reminder that it took years to find SARS. https://www.nature.com/articles/d41586-017-07766-9 https://www.nature.com/articles/d41586-017-07766-9 There

Standard reminder that it took years to find SARS. https://www.nature.com/articles/d41586-017-07766-9 https://www.nature.com/articles/d41586-017-07766-9 There are lots and lots of bat caves.

jacquesm 3y ago
That, plus that the ease with which the virus jumped back to animals (deer, hamsters, mice, ferrets, cats, dogs) makes the search for a reservoir animal very difficult, as well as the fair chance that there were few enough of those (possibly only one) that that part of the evidence chain may well remain broken.
- jahnu 3y ago
  Wouldn't our extensive records of the variants so far make it possible to see if a variant discovered in bats tomorrow is newer than the one that started the original outbreak in humans?
  - jacquesm 3y ago
    If the differences are large enough: yes. If not then it may remain undecided. The closest match found in the wild so far is 96% or so, which is good but not good enough (and it was found in a bat, but relatively far away from the spot where it was first found in humans). I think that is the most recent state of affairs.
    - stringsandchars 3y ago
      > but relatively far away from the spot where it was first found in humans But not far away from humans who had been to where the bat virus was found to bring back samples for analysis and experimentation in their laboratory [1] [1] spoiler alert: the Wuhan Institute of Virology
      - jacquesm 3y ago
        So? That's what they do at that institute. The only reason that that bat was far away from where it was first found in humans is simply because we haven't found a better sample, yet. This was iirc a sample taken long ago, so there was plenty of time for migration. Bats fly insanely long distances and can have multiple roosts. What all lab-leak theory adherents seem to forget: if the Chinese really had ready access to the very earliest strains of COVID they could have easily falsified evidence of where it originated. The fact that this hasn't happened is - especially given what is at stake here - pretty good circumstantial evidence that they not have access to that strain. I suspect it will take a long time (years, maybe as much as a decade) before the whole picture will come out and if not then too bad, it will be one of those things we'll never know. Which is entirely in line with expectations, and with the historical record of other discoveries like that. In the meantime: speculation is pointless. Either you have evidence or you don't. And [] do not confer any special insights unless actually accompanied by a citation, preferably of something that is not written by the same author.
- stringsandchars 3y ago
  > That, plus that the ease with which the virus jumped back to animals It is trivial to tell whether a variant is antecedent - this is how the absurd 'double jump' of lineage A and lineage B was necessary for Worobey to justify his thesis that the wet market was the origin of covid... twice
  - jacquesm 3y ago
    Without commenting on Worobey's thesis: > It is trivial to tell whether a variant is antecedent I'm sure all of the evolutionary biologists would love to have your level of confidence. It's trivial when the differences and the timescales are large (and even then we get it wrong plenty of times). But it isn't trivial at all when the differences are minor and the timescales are close, in fact it can be really, really hard. Fortunately with COVID19 a lot of evidence was gathered in real time and preserved so there are a lot of theories that can be ruled out based on that. One of the hardest problems is to figure out when there is an individual where more than one virus took hold at the same time and genetic material was exchanged between two strains rather than just a mutation. There is some - but inconclusive - evidence that this happened more than once during the COVID pandemic.
    - stringsandchars 3y ago
      > I'm sure all of the evolutionary biologists would love to have your level of confidence. It's easy to say this, as neither you nor I have the requisite knowledge to prove/disprove your assertion. But I read threads like this one [1] or resources like this one [2] and realize that there are experts who are able to distinguish earlier and later variants. Incidentally, I noticed that you edited your first response several times while I wrote this. The tone of what you wrote first was a bit less considered than the what I'm responding to now, but I hope it's ok to just leave it at this. [1] https://nitter.net/ydeigin/status/1695588327540347329 https://nitter.net/ydeigin/status/1695588327540347329 [2] https://github.com/jbloom/PRJNA692319_public https://github.com/jbloom/PRJNA692319_public
      - jacquesm 3y ago
baja_blast 3y ago
False! It took MONTHS to find an intermediate host for both SARS and MERS. SARS1 they found infected civet cats with an almost identical virus within a few months: >”Civet cats, a raccoon dog, and a ferret badger in an animal market in Gunagdong, China, were infected with a coronavirus identical to the one that causes SARS in humans save for an extra 29-nucleotide sequence" which demonstrated that these animals had a very close ancestral virus circulating within their populations. Source: https://zenodo.org/record/3949022#.Y9hn9uzMJqs https://zenodo.org/record/3949022#.Y9hn9uzMJqs. For MERS it took a little longer since by the time they discovered it in dromedary camels only 500 people were infected. But they still found it in less than a year! Source: https://www.eurosurveillance.org/content/10.2807/1560-7917.ES2013.18.50.20662 https://www.eurosurveillance.org/content/10.2807/1560-7917.E...
tripletao 3y ago
You've made this false claim before. I responded correcting you, and you didn't respond to me. At this point, it seems like you're willfully posting misinformation. As I noted previously, the likely proximal zoonotic host for SARS-1 was discovered within about a year. The article that you've linked discusses different related bat viruses. These provide important information about the evolutionary history of the human virus, but are more genetically distant from the human virus than the civet and raccoon dog viruses found within that ~year. https://news.ycombinator.com/item?id=37095934 https://news.ycombinator.com/item?id=37095934
- conception 3y ago
  Ah, fair and interesting. Thanks for pointing this out. I think it's more that it's harder to keep track of when people comment on your stuff. I'll make a note not to share anymore!
  - tripletao 3y ago
    Thanks, and sorry for my impatience; I've seen that claim in enough places (from many other people) that I got frustrated. The absence of a clear proximal host certainly isn't proof that SARS-CoV-2 arose unnaturally, especially since the PRC's preferred origin story (imported on frozen food) would require them to cover that up too. It's not what anyone expected though, since it's different from SARS-1 and MERS.

Standard reminder that it took years to find SARS. https://www.nature.com/articles/d41586-017-07766-9 https://www.nature.com/articles/d41586-017-07766-9 There are lots and lots of bat caves.

jacquesm 3y ago

That, plus that the ease with which the virus jumped back to animals (deer, hamsters, mice, ferrets, cats, dogs) makes the search for a reservoir animal very difficult, as well as the fair chance that there were few enough of those (possibly only one) that that part of the evidence chain may well remain broken.

jahnu 3y ago
Wouldn't our extensive records of the variants so far make it possible to see if a variant discovered in bats tomorrow is newer than the one that started the original outbreak in humans?
- jacquesm 3y ago
  If the differences are large enough: yes. If not then it may remain undecided. The closest match found in the wild so far is 96% or so, which is good but not good enough (and it was found in a bat, but relatively far away from the spot where it was first found in humans). I think that is the most recent state of affairs.
  - stringsandchars 3y ago
    > but relatively far away from the spot where it was first found in humans But not far away from humans who had been to where the bat virus was found to bring back samples for analysis and experimentation in their laboratory [1] [1] spoiler alert: the Wuhan Institute of Virology
    - jacquesm 3y ago
      So? That's what they do at that institute. The only reason that that bat was far away from where it was first found in humans is simply because we haven't found a better sample, yet. This was iirc a sample taken long ago, so there was plenty of time for migration. Bats fly insanely long distances and can have multiple roosts. What all lab-leak theory adherents seem to forget: if the Chinese really had ready access to the very earliest strains of COVID they could have easily falsified evidence of where it originated. The fact that this hasn't happened is - especially given what is at stake here - pretty good circumstantial evidence that they not have access to that strain. I suspect it will take a long time (years, maybe as much as a decade) before the whole picture will come out and if not then too bad, it will be one of those things we'll never know. Which is entirely in line with expectations, and with the historical record of other discoveries like that. In the meantime: speculation is pointless. Either you have evidence or you don't. And [] do not confer any special insights unless actually accompanied by a citation, preferably of something that is not written by the same author.
stringsandchars 3y ago
> That, plus that the ease with which the virus jumped back to animals It is trivial to tell whether a variant is antecedent - this is how the absurd 'double jump' of lineage A and lineage B was necessary for Worobey to justify his thesis that the wet market was the origin of covid... twice
- jacquesm 3y ago
  Without commenting on Worobey's thesis: > It is trivial to tell whether a variant is antecedent I'm sure all of the evolutionary biologists would love to have your level of confidence. It's trivial when the differences and the timescales are large (and even then we get it wrong plenty of times). But it isn't trivial at all when the differences are minor and the timescales are close, in fact it can be really, really hard. Fortunately with COVID19 a lot of evidence was gathered in real time and preserved so there are a lot of theories that can be ruled out based on that. One of the hardest problems is to figure out when there is an individual where more than one virus took hold at the same time and genetic material was exchanged between two strains rather than just a mutation. There is some - but inconclusive - evidence that this happened more than once during the COVID pandemic.
  - stringsandchars 3y ago
    > I'm sure all of the evolutionary biologists would love to have your level of confidence. It's easy to say this, as neither you nor I have the requisite knowledge to prove/disprove your assertion. But I read threads like this one [1] or resources like this one [2] and realize that there are experts who are able to distinguish earlier and later variants. Incidentally, I noticed that you edited your first response several times while I wrote this. The tone of what you wrote first was a bit less considered than the what I'm responding to now, but I hope it's ok to just leave it at this. [1] https://nitter.net/ydeigin/status/1695588327540347329 https://nitter.net/ydeigin/status/1695588327540347329 [2] https://github.com/jbloom/PRJNA692319_public https://github.com/jbloom/PRJNA692319_public
    - jacquesm 3y ago

baja_blast 3y ago

False! It took MONTHS to find an intermediate host for both SARS and MERS. SARS1 they found infected civet cats with an almost identical virus within a few months: >”Civet cats, a raccoon dog, and a ferret badger in an animal market in Gunagdong, China, were infected with a coronavirus identical to the one that causes SARS in humans save for an extra 29-nucleotide sequence" which demonstrated that these animals had a very close ancestral virus circulating within their populations. Source: https://zenodo.org/record/3949022#.Y9hn9uzMJqs https://zenodo.org/record/3949022#.Y9hn9uzMJqs. For MERS it took a little longer since by the time they discovered it in dromedary camels only 500 people were infected. But they still found it in less than a year! Source: https://www.eurosurveillance.org/content/10.2807/1560-7917.ES2013.18.50.20662 https://www.eurosurveillance.org/content/10.2807/1560-7917.E...

tripletao 3y ago

You've made this false claim before. I responded correcting you, and you didn't respond to me. At this point, it seems like you're willfully posting misinformation. As I noted previously, the likely proximal zoonotic host for SARS-1 was discovered within about a year. The article that you've linked discusses different related bat viruses. These provide important information about the evolutionary history of the human virus, but are more genetically distant from the human virus than the civet and raccoon dog viruses found within that ~year. https://news.ycombinator.com/item?id=37095934 https://news.ycombinator.com/item?id=37095934

conception 3y ago
Ah, fair and interesting. Thanks for pointing this out. I think it's more that it's harder to keep track of when people comment on your stuff. I'll make a note not to share anymore!
- tripletao 3y ago
  Thanks, and sorry for my impatience; I've seen that claim in enough places (from many other people) that I got frustrated. The absence of a clear proximal host certainly isn't proof that SARS-CoV-2 arose unnaturally, especially since the PRC's preferred origin story (imported on frozen food) would require them to cover that up too. It's not what anyone expected though, since it's different from SARS-1 and MERS.