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T. Ryan Gregory 🇨🇦 Profile picture
@TRyanGregory
Oct 23, 2024 • 4 tweets • 1 min read • Read on X
So, @arijitchakrav and I have been talking about the idea of "slow COVID", which is a distinct issue alongside severe acute COVID and long COVID.

This means the accumulation of damage that shows up over time, either through repeated infections or persistent infection.
The main distinction between slow COVID and long COVID is that long COVID is clearly associated with debilitating symptoms from the outset. Slow COVID may be more insidious, with organ or immune or cognitive or other function declining gradually over time.
Again, slow COVID could happen as a result of damage from the initial infection that takes time to manifest, through cumulative damage from repeated infections, and/or persistent infection.
We're still working through the ideas and how to model and test the hypothesis. But let's just say, every time I see a study (of which there seems to be a steady flood) that shows organ damage, I think about the potential risk of "slow COVID".

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More from @TRyanGregory

T. Ryan Gregory 🇨🇦 Profile picture
Jun 12
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 🇨🇦 Profile picture
Jun 6
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 🇨🇦 Profile picture
May 27
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
T. Ryan Gregory 🇨🇦 Profile picture
Apr 29
Btw folks, what happened is that Québec saved us all from Poilievre. Bloc voters went Liberal this time to keep him out.

Ontario, not so much. Big gains for the Cons.

BC was where the NDP did best last election, and this time it went Lib and Con.
So, we essentially traded a Liberal minority with progressive parties being very influential to a Liberal minority with a huge Conservative opposition and minimal progressive representation.

The fact that 41.4% voted Con (vs. 43.5% Lib) isn't a good sign either.
Yes, I'm relieved that it's not Poilievre as PM and I'm glad he lost his seat. But beyond that, we're not in a very good place overall. The major rightward shift isn't going to be good, especially when the Liberals eventually lose to the Conservatives.
Read 4 tweets
T. Ryan Gregory 🇨🇦 Profile picture
Apr 1
It's very important to be clear about what is happening in the Canadian election and how progressives need to approach it. 🧵

The LPC surge toward a majority is due primarily to a collapse of support for the NDP and Bloc, and much less so a drop in support for the CPC.

1/ Vote and seat projections for Canada.
Vote and seat projections for Ontario.
Vote and seat projections for Québec.
This means that the Libs are mostly picking up progressive voters who are planning to vote strategically to stop the Cons. They are not picking up huge numbers of "moderate conservatives".

Cons support is generally committed but Libs support isn't.



2/angusreid.org/canadian-elect…
The *winning strategy* for Libs is to make strategic voting by progressives as painless as possible by leaning *leftward*.

The winning approach for progressive voters is to make it clear they cannot be taken for granted and do not agree with rightward drift.

3/
Read 6 tweets
T. Ryan Gregory 🇨🇦 Profile picture
Mar 19
Thoughts on pandemics, inclusion, annexation, Indigenous issues, climate, genocide, and more and the connections I see among them. I fully acknowledge that I am writing this from a position of substantial intersectional privilege.

🧵

1/
I really hoped that the (ongoing) SARS-CoV-2 pandemic would inspire us to make meaningful, positive changes in society. Indeed, early on it seemed like privileged people finally understood what it was like to lack access to things we otherwise take for granted.

2/
Sadly, but perhaps predictably, we instead rushed back to the status quo as quickly as we could. If anything, things are worse now in terms of public health, accessibility and inclusion, and global health equity. Infectious disease has been actively normalized.

3/
Read 10 tweets

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