5 ms·

> 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 j

> 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
    > It's easy to say this, as neither you nor I have the requisite knowledge to prove/disprove your assertion. I actually do have that knowledge, you just speak for yourself. The fact that experts are able to distinguish earlier and later variants doesn't mean that this is trivial, nor does it mean that this is something that is error free. So your statement simply does not stand. Whether or not you can make a statement about the order in which mutations happened (which is the genetic basis for all evolutionary biology) hinges on a large number of factors and not all of those may be in agreement. I've been somewhat involved in a bunch of issues around determining the sequence in which a plant mutated historically and in spite of a good idea of the overall picture the final call was less solidly supported than the parties involved would have liked. And that's before we get into the thorny issues of gaps in the record and sequence alignment, which by themselves can give rise to all kinds of interpretations. > 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. Yes, I added some more information but the gist of it stands: this isn't trivial. Not by a long shot.
    - stringsandchars 3y ago
      > The fact that experts are able to distinguish earlier and later variants doesn't mean that this is trivial So you are arguing with my loose assertion that it is trivial whereas what I should have been more clear about, was that I consider it possible by experts with the requisite expertise.
      - jacquesm 3y ago
        With the caveat that even those experts are sometimes confounded, yes.
pcrh 3y ago
There's nothing difficult about the two lineages at the market. What it indicates is that SARS-CoV2 had been circulating for some time before the pandemic took off. We now know that it can spread asymptomatically. The differences between the lineages is very small, amounting to a few weeks of the same kind of random variation frequently observed in real time during the pandemic. What is does indicate is that those first diagnosed with SARS-CoV2 most likely contracted it from different sources, rather than as a consequence of encountering the same infected person or animal.
- baja_blast 3y ago
  And in fact the two linages only different by 2 bases, something that can occur in a single host, it in no way indicates there were two jumps. All you need is for a virus to be circulating in humans for like a week. As Stanford Biologist Michael Lim points out: >indeed he goes straight from seeing 2 lineages to concluding there were 2 jumps from wildlife days apart. That : (a) assumes the jumps were from wildlife, not people. (b) hides the fact that >2 mutations are being made in each host anyway, so separate events not needed https://twitter.com/michaelzlin/status/1632249640832880640 https://twitter.com/michaelzlin/status/1632249640832880640 >Indeed Worobey seems to think "Lineage A" and "Lineage B" are some profoundly different lineages but the tree he shows confirms they are different by only 2 bases. The "A" root has 2 fewer mutations than the "B" root. He doesn't point this out. Yet he must know. https://twitter.com/michaelzlin/status/1632249637645201408 https://twitter.com/michaelzlin/status/1632249637645201408
  - pcrh 3y ago
    It isn't the fact that there are two mutations that defines two lineages. One lineage is different from the other at two positions. The mutations defining these two lineages could have occurred in either animals or humans. What it does imply is that SARS-CoV2 was circulating at the Wuhan market for at least weeks or months before the first samples were collected. However, two base changes is very little data from which to construct a phylogenetic relationship or make "molecular clock" calculations.

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
  > It's easy to say this, as neither you nor I have the requisite knowledge to prove/disprove your assertion. I actually do have that knowledge, you just speak for yourself. The fact that experts are able to distinguish earlier and later variants doesn't mean that this is trivial, nor does it mean that this is something that is error free. So your statement simply does not stand. Whether or not you can make a statement about the order in which mutations happened (which is the genetic basis for all evolutionary biology) hinges on a large number of factors and not all of those may be in agreement. I've been somewhat involved in a bunch of issues around determining the sequence in which a plant mutated historically and in spite of a good idea of the overall picture the final call was less solidly supported than the parties involved would have liked. And that's before we get into the thorny issues of gaps in the record and sequence alignment, which by themselves can give rise to all kinds of interpretations. > 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. Yes, I added some more information but the gist of it stands: this isn't trivial. Not by a long shot.
  - stringsandchars 3y ago
    > The fact that experts are able to distinguish earlier and later variants doesn't mean that this is trivial So you are arguing with my loose assertion that it is trivial whereas what I should have been more clear about, was that I consider it possible by experts with the requisite expertise.
    - jacquesm 3y ago
      With the caveat that even those experts are sometimes confounded, yes.

pcrh 3y ago

There's nothing difficult about the two lineages at the market. What it indicates is that SARS-CoV2 had been circulating for some time before the pandemic took off. We now know that it can spread asymptomatically. The differences between the lineages is very small, amounting to a few weeks of the same kind of random variation frequently observed in real time during the pandemic. What is does indicate is that those first diagnosed with SARS-CoV2 most likely contracted it from different sources, rather than as a consequence of encountering the same infected person or animal.

baja_blast 3y ago
And in fact the two linages only different by 2 bases, something that can occur in a single host, it in no way indicates there were two jumps. All you need is for a virus to be circulating in humans for like a week. As Stanford Biologist Michael Lim points out: >indeed he goes straight from seeing 2 lineages to concluding there were 2 jumps from wildlife days apart. That : (a) assumes the jumps were from wildlife, not people. (b) hides the fact that >2 mutations are being made in each host anyway, so separate events not needed https://twitter.com/michaelzlin/status/1632249640832880640 https://twitter.com/michaelzlin/status/1632249640832880640 >Indeed Worobey seems to think "Lineage A" and "Lineage B" are some profoundly different lineages but the tree he shows confirms they are different by only 2 bases. The "A" root has 2 fewer mutations than the "B" root. He doesn't point this out. Yet he must know. https://twitter.com/michaelzlin/status/1632249637645201408 https://twitter.com/michaelzlin/status/1632249637645201408
- pcrh 3y ago
  It isn't the fact that there are two mutations that defines two lineages. One lineage is different from the other at two positions. The mutations defining these two lineages could have occurred in either animals or humans. What it does imply is that SARS-CoV2 was circulating at the Wuhan market for at least weeks or months before the first samples were collected. However, two base changes is very little data from which to construct a phylogenetic relationship or make "molecular clock" calculations.