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Comment by jacquesm | Hacker News Reader

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.

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> 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

[2] https://github.com/jbloom/PRJNA692319_public

> 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.

> 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.

With the caveat that even those experts are sometimes confounded, yes.

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