An argument that only something that isn't descended from within the (very large and expanding) Omicron clade can get a new @WHO Greek letter isn't consistent with the stated criteria, and it misses the point of how evolution works.

1/
Think about birds. In phylogenetic terms, they are nested within "reptiles" (and thus *are* reptiles if "reptiles" is to be a clade and not paraphyletic).

(I talked about clades, monophyly, and paraphyly here: )

2/
BUT, we talk about birds separately from "reptiles" all the time. Ornithology is not part of herpetology. Why? Because the rate of change in various traits in the avian lineage is much faster and they are quite different from other "reptiles".

3/
With SARS-CoV-2 variants, you could get something very different if it evolves from a deeply divergent branch and not from within Omicron, OR you get some lineages of Omicron that change a lot very quickly. (Also, recombination across distinct lineages could do it).

4/
The Greek naming system was introduced when it was just deeply divergent lineages. But now we have rapid diversification within a clade and the naming hasn't kept pace.

5/

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More from @TRyanGregory

Nov 4
Think back to early November 2021. People thought "Ok, Delta was bad, but that is probably it now."

THEN OMICRON HIT.

What makes everyone so totally confident, in November 2022, that Omicron was the last major new variant? COVID deaths in the US, the...
I will remind everyone that there are two major ways that new variants evolve: within individual hosts with persistent infections, and among hosts at the level of the host population. The past major new variants (ones that got Greek letters) probably evolved within hosts.
Evolution within hosts can be for different traits than among hosts. Within a host, it's a matter of competition for how well cells are infected, how quickly replication occurs, how many copies get made, etc., relative to different versions of the virus in the same individual.
Read 11 tweets
Nov 2
Never heard of this guy before today (I know, lucky). But omg. Dude uses shampoo from a bo...
How did I miss this entire saga?

avclub.com/guy-who-got-ro…
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Nov 1
I'm some ways "season" is like "latitude". Lots of things correlate with it, but it itself isn't a thing, causally speaking. What they both actually represent is a combination of temperature, precipitation, daylight, etc.
With COVID, it's not "seasonal" like annual flu -- we've had 4 waves already this year -- but there are effects on host behaviour caused by temperature, precipitation, daylight, etc. Whether we gather indoors. Whether windows are open. Things that can affect viral spread.
So, no, SARS-CoV-2 is not a seasonal virus. But yes, there are patterns associated with factors that vary across seasons. That's why comparisons between the summer 2022 wave (BA.5) and winter 2021/2022 (BA.1) are misleading if they're used to infer that new variants are milder.
Read 15 tweets
Oct 31
Much important discussion going on within Indigenous communities about how membership is defined and determined. It's not my place to weigh in, but as to the question of whether any European groups allow membership based on DNA or distant ancestry: yep.

themacgregordnaproject.blogspot.com/?m=1
For the record, I don't know if I would count as a MacGregor. I've not done any DNA test, and the farthest back anyone has traced my own Gregory line (obviously speaking patrilineally) is 7 generations to the first arrival in Canada.
Obviously the stakes are not high in terms of Scottish clan membership for a 7th generation Canadian. I'm not drawing any comparison with Indigenous issues. But it's interesting in some ways that Europeans do, in some cases, look at DNA to determine membership in a group.
Read 4 tweets
Oct 29
Where is @CDCDirector? Tested positive 8 days ago. If she's following @CDCgov guidelines, why wasn't she back to work after 5 days? If her infection is mild, why isn't she out there encouraging booster uptake?
And don't be stupid. I don't want her to be seriously ill. I'm asking why her agency's policies don't appear to be applied to her.
Closing comments. Trolls and people who refuse to understand the point are getting annoying.
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Oct 28
Just a reminder that the CDC is way behind what variant trackers on Twitter share everyday. Follow @RajlabN, @DGBassani, @CorneliusRoemer, @EllingUlrich, @yunlong_cao, @Mike_Honey_, @LongDesertTrain, @dfocosi.
Stay up to date using these tools.

@RajlabN's variant trackers:

public.tableau.com/app/profile/ra…
Read 6 tweets

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