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Re:Some experts suggest Omicron variant may have evolved in ... by timr on Thursday December 02, 2021 @01:31PM (#29420267)
Your options are fine, but nowhere near a comprehensive set. You left out an obvious option, for example:

4. Evolution of a lineage that we didn't detect until now because it wasn't common.

We need to stop making the assumption that our surveillance systems are comprehensive. They're pretty bad, actually -- and they're generally incredibly biased in what they're looking at. Even if we were doing unbiased random sampling and sequencing, we'd have to do huge volumes of it to reliably detect rare strains.

(aside: and if we did do that, we'd be in non-stop panic mode, because we'd be finding a new strain every day.)

Re:Some experts suggest Omicron variant may have evolved in ... by onychomys on Thursday December 02, 2021 @01:41PM (#29420420)
But we'd have to be missing a huge number of related strains to make the phylogeny look like that. The important thing isn't that we found a new strain now, it's that the strain is most closely related to very early wildtype.
Re:Some experts suggest Omicron variant may have evolved in ... by timr on Thursday December 02, 2021 @02:07PM (#29420915)
> But we'd have to be missing a huge number of related strains to make the phylogeny look like that

Define "huge". There are about ~30 mutations on the spike protein from the closest known relative, and there's a fairly strong selective pressure against the wild type (both from vaccine and natural infection). I think it's quite probable that we missed a few months of evolution of a strain circulating in a single-digit percentage of people.

This is particularly true when you consider that this strain has S-gene dropout (Delta does not), and was probably dismissed as Beta and never targeted for sequencing by most labs. That's why I meant by my original comment that we're biased about what we look at.

Re:Some experts suggest Omicron variant may have evolved in ... by whimsicalism on Thursday December 02, 2021 @01:56PM (#29420710)
Well yeah, many of the places with the worst testing coverage are probably close to each other geographically.
Re:Some experts suggest Omicron variant may have evolved in ... by nostrademons on Thursday December 02, 2021 @08:12PM (#29425413)
Or the population that it evolved in is isolated, so it never escaped back into the developed world until now. Somewhat unlikely given how interconnected the world is now, but it is Africa after all.
Re:Some experts suggest Omicron variant may have evolved in ... by ErikCorry on Thursday December 02, 2021 @01:41PM (#29420433)
Denmark and Iceland sequence every single positive sample. Currently 4k per day for Denmark. So I think there's more surveillance than you think.
Re:Some experts suggest Omicron variant may have evolved in ... by timr on Thursday December 02, 2021 @02:03PM (#29420846)
Yeah, some do. But consider that there are at least millions of new infections a day, globally...
Re:Some experts suggest Omicron variant may have evolved in ... by downWidOutaFite on Thursday December 02, 2021 @02:15PM (#29421022)
Also consider how interconnected the world is that Delta spread around the globe in a few months.
Re:Some experts suggest Omicron variant may have evolved in ... by timr on Thursday December 02, 2021 @02:38PM (#29421346)
Oh, definitely. It's fairly obvious to anyone who understands molecular clocks that this strain is already widely spread.

We're panicking and closing borders and doing untold damage because...we continue to overestimate our ability to see what nature is doing in an unbiased way.

Re:Some experts suggest Omicron variant may have evolved in ... by dkonofalski on Thursday December 02, 2021 @05:19PM (#29423562)
That wouldn't happen, even with our substandard testing, unless the strain somehow had very low ability for transmission and then only evolved that in this last jump which is not likely. Since there are multiple variations from the older strain, we'd have seen at least some of the new variations along the way.
Re:Some experts suggest Omicron variant may have evolved in ... by manojlds on Friday December 03, 2021 @01:31AM (#29427238)
I still can't believe that US, where it's been rampant, hasn't been a place to report a new variant of concern for the first time, but UK, India, SA (and other like Peru?) have.