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T. Ryan Gregory Profile picture
@TRyanGregory
Oct 23 • 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
Oct 22
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&…
2) Heart?

scholar.google.com/scholar?hl=en&…
Read 15 tweets
T. Ryan Gregory Profile picture
Sep 17
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.
2. The last Greek letter was given in November 2021. "Omicron" variants are **far** more diverse and divergent than any of the others that received Greek letters, yet not even the ones requiring updates to vaccines (XBB.1.5, JN.1/KP.2) were named. Image
Read 7 tweets
T. Ryan Gregory Profile picture
Sep 9
The minimizer position is committed to every one of these assumptions being true. The cautious position is the right one if even one of them is false. 🧵
Required assumptions:

1. Immunity against severe illness will be long-lasting or can be maintained at low risk (vaccination or truly mild infection).

2. Most people are not at risk of long COVID.

3. There is no cumulative damage or risk associated with repeated infection.
Required assumptions:

4. Replication-competent virus does not persist in different tissues except in very rare circumstances and/or does no damage to organs in which it occurs.

5. Wastewater is a signal mostly of asymptomatic, or at most mild, short-lived infection.
Read 7 tweets
T. Ryan Gregory Profile picture
Sep 2
As we head into the new school year and then into winter, a reminder about these articles focused on actually doing something to keep our kids and other loved ones healthy. 🧵
August 2024.

"Protecting HCWs and patients: An impossible fix, or an essential one?"

calgaryherald.com/opinion/column…
December 2022.

"We don't know what's causing the tsunami of sick kids, but we'd better figure it out fast"

(So... how has that immunity debt repayment plan worked out after nearly two years since we wrote this?)

calgaryherald.com/opinion/column…
Read 5 tweets
T. Ryan Gregory Profile picture
Aug 31
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.
Read 5 tweets
T. Ryan Gregory Profile picture
Aug 19
For my reporter friends who are still writing about SARS-CoV-2 variants (thank you!), here are some notes that I hope are helpful.

🧵
* Pretty much everything circulating right now is a descendant of BA.2.86 (Pirola), which was a highly divergent variant that evolved within a single, chronically-infected host.

* BA.2.86 was descended directly from BA.2 and had about 30 new spike mutations.
* BA.2.86 itself was not very successful. What we said at the time was that its descendants would be the real issue.

* JN.1 (aka BA.2.86.1.1) had one additional spike mutation and was successful. Pretty much everything around now is a descendant of JN.1.
Read 7 tweets

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