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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.
68 subscribers
Nov 8 • 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 • 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 • 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 • 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 • 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 • 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 • 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 • 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.
Sep 9 • 7 tweets • 1 min read
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.
Sep 2 • 5 tweets • 1 min read
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…
Aug 31 • 5 tweets • 2 min read
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.
Aug 19 • 7 tweets • 2 min read
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.
Aug 13 • 8 tweets • 3 min read
When making a decision regarding who is and who isn't a reliable source of information about SARS-CoV-2, one can look at how often they have said either "Well, I didn't expect that" versus "Yes, as I have been saying for a while now".

Here's a notable example. 🧵 I want to bring up a thread I wrote *a year ago*, on the then newly-discovered (by @shay_fleishon) BA.2.86 variant.

Aug 10 • 4 tweets • 1 min read
Introducing three exciting new approaches to public health*! 🧵

1. Epidemiastrology.
2. Viralchemy.
3. Common-cold reading.

(* For personal career advancement purposes only. No accountability allowed.) 1. Epidemiastrology: making incorrect predictions about SARS-CoV-2 waves based on nonsense assumptions about mechanisms.
Aug 9 • 9 tweets • 2 min read
Lots of SARS-CoV-2 in wastewater. Far fewer hospitalizations than in early waves of this size.

Why?

Could be several (non-mutually-exclusive) things. We've talked about most of these at various times before, but here's a rundown of some hypotheses.

🧵 H1. Hospitalizations lag wastewater, so it's just a matter of time.

I don't think this is it, to be honest. Hospitals haven't been overrun during waves for long time now and wastewater levels have been high for a while already.
Jul 11 • 4 tweets • 2 min read
If someone says that SARS-CoV-2 variant evolution is slowing down, they can safely be ignored as a source of non-bogus information. Evolutionary tree of SARS-CoV-2 variants.
Spike mutations over time.
Mutations over time.
Immune escape over time. More on what is actually happening with SARS-CoV-2 evolution:

Jul 7 • 20 tweets • 5 min read
SARS-CoV-2 provides an unprecedented opportunity to watch evolution occur in real time. It also happens to be showing the pervasiveness of many misconceptions about evolution, even among scientists with limited knowledge of evolutionary biology. Here's a list and explanations. 🧵 Misconceptions about evolution on display with SARS-CoV-2:

1. Typological thinking.
2. Variation seen as noise rather than signal.
3. Teleology.
4. Orthogenesis.
5. Not understanding how natural selection works.
6. Ignoring Orgel's second rule.
7. Myths about human evolution.
Jul 4 • 5 tweets • 1 min read
We sure went quickly from "it's just another seasonal respiratory virus like flu and colds" to "several surges per year are to be expected as immunity wanes and immune-escaping variants evolve".

Reminder 1: that waning, escaped immunity is what is currently keeping severity low. Reminder 2: Vaccines become outdated as new variants evolve, and there is no effort to be predictive with updated vaccines. They're generally already behind variant evolution before they even roll out. We could do better than this.
Jun 24 • 12 tweets • 2 min read
Lower acute severity of SARS-CoV-2 vs. 2020-2022 is welcome, but there's a danger in reading too much into it, in the same way that it's misguided to deny climate change because it's been cold where you live.

A few thoughts as to why our optimism should be cautious.

🧵 1. The lower acute severity seen right now is very likely due to host immunity, not to a reduction in inherent virulence. That immunity comes from two sources: vaccination and past infection (or both, so-called "hybrid immunity").

Cont'd...
Jun 23 • 7 tweets • 3 min read
Confused about the variants you're hearing about most right now? Here they are, explained. 🧵 XBB.1.5 ("Kraken")

What it is: A descendant of XBB, which was a recombinant between two BA.2 lineages.

Status: Not circulating anymore.

Why relevant: It is the variant targeted by current vaccine boosters. XBB.1.5 vs. XBB mutations. From cob-spectrum.org
Jun 18 • 24 tweets • 5 min read
We have both continuous and continual SARS-CoV-2 variant evolution happening. What do I mean? 🧵 Viruses evolve at (at least) two levels: among hosts and within hosts. Among hosts, the main determinant of viral fitness (i.e., reproductive success and continued existence of that lineage) is getting into new hosts.