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T. Ryan Gregory πŸ‡¨πŸ‡¦ Profile picture
@TRyanGregory
Aug 31, 2024 β€’ 5 tweets β€’ 2 min read β€’ Read on X
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If anyone says "It's all still Omicron", "The current variants aren't that different", "SARS-CoV-2 is running out of evolutionary space", or "The current wave is finally over!", show them these. 🧡 Evolutionary tree showing SARS-CoV-2 variants. It is a radial tree (the branches curve to fit a circular shape) scaled to divergence (the farther from the centre, the more mutations). It shows wild type, Alpha, Beta, Gamma, Delta, Epsilon, Zeta, Eta, Theta, Iota, Kappa, Lambda, and Mu all clustered in a small area, and an enormous diversity and divergence within "Omicron". We currently (Aug. 2024) are dealing with highly divergent variants descended from JN.1. Reminder that all WHO Greek letters were assigned between May and November 2021 and none since. From Nextstrain.org.

Graph showing mutations in SARS-CoV-2 variants over time. If anything, the current variants have *higher* than expected numbers of mutations (i.e., they are above the trend line). The virus is clearly not running out of evolutionary space. From Nextstrain.org.
Spike mutations over time. Each cluster of new variants shows a major leap (followed by a period of smaller-scale divergence), with the current variants being highly divergent. From Nextstrain.org.

Diagram showing how more infections leads to more variants evolving. More infections mean: 1) more viral replication, which means more mutations added to the gene pool, 2) more persistent infections, which means more within-host evolution, 3) more coinfections, which means more recombination, 4) a larger population size, which means stronger natural selection, 5) partial immunity that waves, which means a shifting immune landscape in which variants evolve, 6) more chance of reverse zoonosis as the virus infects and then evolves in another susceptible species.
Graph of COVID-19 hospitalizations in Canada throughout the pandemic. At each low period, there is some expression of relief or a confident assertion that the pandemic is over, followed by each subsequent peak labelled with "No one could have foreseen this". The final entry, at a low point in spring 2024, is marked "This looks like a good place to stop reporting", as that is where the data were no longer being posted to Our World In Data.
@rwsanders Btw, that's still ~1,000 deaths per week.
@rwsanders Oh, and yes they are correlated on that graph. The ratio has gone down significantly though. Which, again, we've all noted and discussed many times.

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More from @TRyanGregory

T. Ryan Gregory πŸ‡¨πŸ‡¦ Profile picture
Jan 24
I need Canadians to think about what is happening here at home. Carney is cutting the very agencies we need more than ever as things erode in the US.

Wake. Up.

🧡
ctvnews.ca/canada/article…
ctvnews.ca/ottawa/article…
Read 8 tweets
T. Ryan Gregory πŸ‡¨πŸ‡¦ Profile picture
Dec 5, 2025
Well, it's that time again. Meet "Cicada", BA.3.2* (including descendant RE.*). This one has been underground for years (its ancestor BA.3 hasn't been circulating since early 2022, and didn't do much then either) but is now emerging as a contender for the next major lineage.
Volunteer variant trackers have been watching this one since March, with it popping up around the world throughout November. It's another highly divergent variant (50 spike mutations) that evolved within a chronically infected host.

Read 6 tweets
T. Ryan Gregory πŸ‡¨πŸ‡¦ Profile picture
Oct 5, 2025
There is growing interest in possible links between SARS-CoV-2 and cancer. I strongly recommend this video series with @arijitchakrav which discusses why it might be even worse.

🧡

Part 1:

Part 2:

Part 3:

Read 4 tweets
T. Ryan Gregory πŸ‡¨πŸ‡¦ Profile picture
Jun 12, 2025
Two new variants are competing for dominance: NB.1.8.1 and XFG. We recently nicknamed NB.1.8.1 "Nimbus", and it's pretty clear that XFG deserves a nickname as well. Keeping with the meteorological theme, XFG = "Stratus".

Here's some more info about Nimbus and Stratus. 🧡

1/
There are two main ways by which divergent variants may evolve within single hosts: evolution during chronic infection and recombination during simultaneous infection with more than one variant. Nimbus (NB.1.8.1) and Stratus (XFG) have both mechanisms in their ancestries.

2/
Stratus (XFG) is a recombinant of LF.7 x LP.8.1.2 -- both of which descendants of BA.2.86, which itself had evolved within someone infected for ~2 years.

LF.7 = JN.1.16.1.7 = BA.2.86.1.1.16.1.7

LP.8.1.2 = JN.1.11.1.1.1.3.8.1.2 = BA.2.86.1.1.11.1.1.1.3.8.1.2

3/ Stratus ancestry diagram summarizing the info given in the main text.
Read 10 tweets
T. Ryan Gregory πŸ‡¨πŸ‡¦ Profile picture
Jun 6, 2025
Nimbus (NB.1.8.1) is getting a fair bit of attention, but it's not the only SARS-CoV-2 variant worth watching. Here's a link to info about a few more, all of which have arisen either through within-host evolution during chronic infection and/or within-host recombination.

🧡

1/
First, a reminder that Nimbus (NB.1.8.1) is a triple recombinant with both BA.2.86 and XBB ancestry -- that is, it has multiple recombination events and chronic infections in its evolutionary history. Here's a thread I wrote about it:



2/
Another that is very competitive is XFG, which is a recombinant of two Pirola lineages (LF.7 x LP.8.1.2).

Head over to BlueSky to see the post by Josette Schoenmakers on the XFG vs. NB.1.8.1 battle for dominance.



3/bsky.app/profile/josett…
Read 4 tweets
T. Ryan Gregory πŸ‡¨πŸ‡¦ Profile picture
May 27, 2025
Meet "Nimbus", aka SARS-CoV-2 variant NB.1.8.1.

🧡

1/ Diagram showing the ancestry of Nimbus (NB.1.8.1). The evolution of NB.1.8.1 has including three recombination events, including XBB (Kraken) and BA.2.86 (Pirola) lineages.
Evolutionary tree of SARS-CoV-2 variants showing the small fraction of diversity covered by every variant with a Greek letter except "Omicron", and the enormous diversity within "Omicron", including Nimbus NB.1.8.1.
The last variant to receive an informal nickname was BA.2.86 "Pirola" nearly two years ago, back in August 2023. Since then, it has been a prolonged "variant soup" phase, with descendants of BA.2.86 arising, gaining prominence, and then falling in frequency.

2/ Tweet from August 18, 2023 with the nickname "Pirola" for BA.2.86.
A prolonged variant soup phase involving the Pirola clan does not mean there was no within-host evolution occurring. It just meant that nothing had gotten back into the general population that could compete with the many, many descendants of BA.2.86.

3/
Read 14 tweets

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