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T. Ryan Gregory 🇨🇦 Profile picture
T. Ryan Gregory 🇨🇦
@TRyanGregory
Professor of evolutionary biology. I would like there to be less death, pestilence, war, and famine. Assume sarcasm. No one could have foreseen this. He/him.
69 subscribers
Jun 12 • 10 tweets • 3 min read
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/
Jun 6 • 4 tweets • 2 min read
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/
May 27 • 14 tweets • 4 min read
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.
Apr 29 • 4 tweets • 1 min read
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.
Apr 1 • 6 tweets • 2 min read
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…
Mar 19 • 10 tweets • 2 min read
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/
Mar 8 • 10 tweets • 2 min read
Please, stop making these terrible arguments in order to dismiss threats of annexation by the US. 🧵

1. "He's just joking, trolling, negotiating, or being Donald."

Clearly not. Stop it.

1/ 2. "Trump can't just declare war on Canada."

He wouldn't bother and he doesn't need to. The last time the US formally declared war was 1942. See every US invasion or occupation since WW2.

2/
Feb 17 • 12 tweets • 3 min read
I'm sure infectious disease minimizers are attributing the record-shattering surge of severe flu this year to "immunity debt". Let's think this through, shall we?

🧵

1/ 1. Serious mitigations ended more than 4 years ago. Why would immunity debt only kick in now? And why wasn't 4 flu seasons without mitigations enough to repay whatever "debt" there was?

2/
Feb 16 • 4 tweets • 1 min read
🧵

Just to recap what is happening, since public health has gone AWOL:

* This is the worst flu season in 15 years. Not just number of cases but number of *severe* cases.

1/ * H5N1 ("avian flu") is getting further out of control in the US. It is getting closer and closer to a human-to-human transmission outbreak.

* Measles is resurgent thanks to low vaccination rates.

* Tuberculosis is making a comeback.

* Many norovirus outbreaks.

2/
Jan 18 • 4 tweets • 1 min read
As you read more and more reports of uncommon pathogens infecting a lot of people, or common pathogens surging far more than usual and/or having unusually severe effects, please remember that this is what immunity theft predicts and what we've warned about for years.

1/ By contrast, "immunity debt" or "post-pandemic normalizing of levels" as an explanation makes less and less sense as more time goes by. In 2025, it is absurd to still be talking of new surges of illness being due to the lack of immunity from mitigations that ended years ago.

2/
Jan 15 • 5 tweets • 1 min read
Lots of things in biology correlate with "latitude" (biodiversity, population size, body size, etc.), but "latitude" itself isn't a thing in and of itself. What actually matters is photoperiod, temperature, precipitation, etc. That's how we should think of "seasonal" as well.

1/ Viral transmission may be strongly and predictably "seasonal", mostly occurring during certain times of the year (flu, RSV), but it's not either-or. Other viruses may be common year-round but also increase at certain times of the year.

2/
Jan 12 • 10 tweets • 2 min read
So, I'm not sure the American right has thought through the implications of annexing Canada yet.

A few things to consider...

1/ First of all, Canada has a slightly larger population than California, so presumably we'd get at least 54 electoral college votes in presidential elections. Polls here showed that about 61% of Canadians would have voted for Harris and 21% for Trump.



/2globalnews.ca/news/10830218/…
Dec 5, 2024 • 4 tweets • 1 min read
(Sarcasm alert) The way viral evolution works is that if you have a naïve idea of how it works and that helps with calm-mongering, that's how it works. Need some examples? 🧵 For example, if it helps with calm-mongering to think that viruses have to evolve to become mild or else they will drive their hosts and themselves extinct, that must be what happens. Don't let actual evolutionary biologists convince you otherwise! (Sarcasm)
Nov 8, 2024 • 8 tweets • 2 min read
One side is consistently painted as violent and the other as being unsafe. Is that accurate? Well, all of these happened on video in Ontario, Canada. 🧵 Attacking with a nail gun while shouting "All Palestinians will die".

Nov 4, 2024 • 4 tweets • 1 min read
How sure are you that only certain people are susceptible to severe acute COVID, and that you're not one of them?

What is your level of certainty that only specific people are vulnerable to long COVID, and that you're not one of them?

1/ Are you certain that repeated SARS-CoV-2 infections won't have cumulative effects?

How confident are you that you don't, or won't ever, harbour a persistent SARS-CoV-2 infection?

Are you totally convinced that SARS-CoV-2 will necessarily become mild and seasonal?

2/
Nov 4, 2024 • 17 tweets • 4 min read
Beyond "immunity debt".

In what ways could SARS-CoV-2 be involved in surges of other infectious diseases like RSV, tuberculosis, fungal infections, Mycoplasma, etc.?

Here is a list of additional hypotheses, all increasingly supported in the scientific literature.

🧵 H1. Temporary immune effects of recent SARS-CoV-2 infection increase susceptibility to other infections.
Nov 3, 2024 • 20 tweets • 4 min read
"Punk variants" and "eek soup". 🧵 I've written many times about how viral evolution occurs at two levels: within hosts (intrahost) and among hosts (interhost).

Oct 30, 2024 • 7 tweets • 2 min read
On tuberculosis. I'm sure we'll be hearing a lot more about how lockdowns caused immunity debt or meant that people weren't getting tested. Here are four additional hypotheses that will get very little attention in the reporting:

🧵 H1. Temporary immune effects of recent SARS-CoV-2 infection increase susceptibility to TB.

journals.plos.org/plosone/articl…
Oct 23, 2024 • 4 tweets • 1 min read
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.
Oct 22, 2024 • 15 tweets • 4 min read
Case in point about denialism, when I post this kind of thing , they'll screenshot and go on a rant about how I don't understand stuff. (Ironically, they demonstrate both poor reading comprehension and a lack of understanding of humour).

Here's why it's denialism 🧵 1) Does SARS-CoV-2 affect lungs? Check the literature for yourself:

scholar.google.com/scholar?hl=en&…
Sep 17, 2024 • 7 tweets • 2 min read
Here's the full pandemic picture based on wastewater surveillance in Canada. A few things of note (most of which I have discussed previously several times): 🧵 Wastewater signal in Canada since 2020, with each peak labelled with the relevant variants and low points highlighted. 1. The story isn't just about peaks, it's about the lack of lows. At best, there have been six periods of lower activity, but really there have only been two decent lulls that were not still at a fairly high baseline and weren't immediately followed by another peak. Wastewater signal in Canada since 2020, with each peak labelled with the relevant variants and low points highlighted. The two real lows were between Alpha and Delta in summer 2021 and between the XBBs and JN.1 in summer 2023.