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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.
Renee Despres, PhD, MPH Profile picture Gus Rousonelos Profile picture Karen Salitis 🇺🇦🇺🇲🇺🇦🇺🇸🇺🇦 Profile picture Martin Leuschen Profile picture David E. Anderson Profile picture 65 subscribed
Apr 4 • 4 tweets • 2 min read
The best we get now is *relative* lows. Here are numbers of hospital patients with COVID in Canada. It's as low as it has been since the first Omicron wave (early 2022), on par with the relative lull of mid-summer 2023. But still much higher than summer 2020 and summer 2021. Hospitalizations in Canada *Maybe* it will continue to drop as thr weather warms and if there are no new major variants that displace JN.1* in the meantime (fingers crossed, and wastewater signal is low), but the reality is that the baseline has never come back down in Canada post-Omicron.
Mar 4 • 14 tweets • 4 min read
Let's be clear about what happened here. 🧵

1. Israeli real estate companies held Jews-only events to sell land in Israel and contested (Jerusalem) or occupied (West Bank) territories in Palestine.

1/ Note that some of the events are taking place in synagogues and some include properties that are within the illegally occupied West Bank. Other events have been held at public venues.

2/
Feb 7 • 7 tweets • 2 min read
Measles touted as an example of the effectiveness of working out one's immune system muscle.

A few reminders about measles...

🧵 "For some bugs, once you've fought it once, your muscles are so strong against it they may never need another work out to fend it off (e.g. measles, smallpox" Measles has been known for 1,000 years and it still hasn't evolved to be benign.

pubmed.ncbi.nlm.nih.gov/36414136/
Feb 4 • 8 tweets • 2 min read
Now that Pirola clan (BA.2.86 and descendants, most notably JN.1*) is the dominant variant lineage globally, the question arises as to whether it might undergo recombination with earlier XBB lineages.

Yep. Already has.

🧵 So far...

Pirola x Arcturus:
XDK = JN.1.1.1 x XBB.1.16.11

Pirola x Eris:
XDD = JN.1 x EG.5.1.1
XDS = JN.3.2.1 x EG.5.1.3

Pirola x Kraken:
XDN = JN.1. x JD.1*
XDR = JN.1.1 x JD.1.1.1

Pirola x Hyperion:
XDP = JN.1.4 x FL.15
Feb 1 • 6 tweets • 2 min read
Here are some excellent threads about more highly divergent BA.2 lineage variants showing up after having evolved within a single host with a chronic infection. Within-host evolution is going to be an increasingly important issue.

🧵
Jan 28 • 5 tweets • 2 min read
Whoa. Japan. Small samples, but obviously do not want an HK.3 wave on top of JN.1 or even just a sustained high baseline.

Reminder:

JN.1 (Pirola clan) = BA.2.86.1.1

HK.3 (Eris + FLip) = EG.5.1.1.3 asahi.com/ajw/articles/1…
Jan 19 • 12 tweets • 3 min read
Now, consider the *possibility* that a) repeated infection is rolling the dice that may eventually lead to long COVID and/or b) it's not "long COVID" vs. "no problem", but more of a continuum in duration and severity.

Immune damage in Long Covid
science.org/doi/10.1126/sc… As I've said, and if we're insisting on using the rhetoric of fiscal metaphors, "immunity theft" can be small and brief (petty immunity theft) all the way to severe and long-term (grand immunity theft). It all adds to negative effects on public health.
Jan 14 • 5 tweets • 1 min read
I guess there's a small chance JN.1 will be named Pi after the upcoming WHO TAG-VE meeting, but I doubt it would happen for several reasons:

1. That would be the first new Greek letter and first acknowledged variant of concern (VOC) in more than 2 years.

1/ 2. It would not really change anything in a practical sense.

3. It's very late to be naming JN.1 now and would show that naming is not a warning system but is applied after the fact. It would be like naming a hurricane after it has already made landfall.
Jan 13 • 8 tweets • 3 min read
Just a reminder that the following are unprecedented in all of human history and pre-history:

* 8 billion hosts.
* Global travel.
* Older population thanks to long lifespans.
* Repeated infections up to several times per year.
* Extremely dense populations, mostly indoors.

🧵

Human population size has grown extremely rapidly over the past few centuries.
Lifespans have increased dramatically since 1900.
Global travel has risen enormously since 1950. This all means that past pandemics are, at best, a very weak guide for what will happen with this one.

Yes, four of the human coronaviruses cause common colds. And three of them are deadly, two of which have caused pandemics within the past 20 years (SARS1, SARS2).
Jan 4 • 27 tweets • 7 min read
‘Pirola’ JN.1 is the probable future of the COVID pandemic, experts warn—but you didn’t hear it from the WHO

by @ErinMPrater

A few quick thoughts... 👇🧵

fortune.com/well/2024/01/0… First, I'll just point out that we had exactly the same issue with XBB.1.5 (Kraken) a year ago.



The Kraken COVID variant isn’t different enough from other Omicrons to get a Greek letter, WHO official saysfortune.com/well/2023/01/1…
Jan 3 • 9 tweets • 3 min read
On the claim that "We've been living alongside pathogenic viruses and bacteria like this for millennia [or even millions of years]"

Two things that matter a great deal for multiple evolutionary and epidemiological reasons: number of hosts and movement of hosts.
Human population growth through history.
Global travel since 1950. Why number of hosts and how many/how often/for how long they are infected and how much they move around matters in viral evolution:

1. More viruses replicating means more errors will occur by chance. That is, more mutations will be added to the viral gene pool.
Jan 1 • 4 tweets • 1 min read
I did, and I specifically meant that the near-exclusive XBB lineage dominance is ceding to a new dominant clade, namely the lineage derived from BA.2.86. I've also pointed out many times that there will be recombination between Pirola and XBB*. XBB was the first recombinant lineage to reach be successful, and indeed almost everything circulating for a year has been derived from it. That era is over as JN.1, which is not a recombinant, is now the dominant variant.

So, the era of recombinants (XBB) is over.
Dec 29, 2023 • 10 tweets • 2 min read
Viruses have no strategy. Evolution has no foresight and is not a process of linear change along a single trajectory. Variation arises at random with respect to whether it will be beneficial, deleterious, or neutral. Fitness depends on the current environment, not the future. There is no basis in experience or theory for assuming that viruses always evolve to become more benign because otherwise they will kill off their hosts. Driving hosts exctinct is an entirely possible outcome. Viruses don't know anything, plan anything, or care about anything.
Dec 29, 2023 • 14 tweets • 3 min read
We're *still* seeing simplistic takes on "immunity debt" to explain any surge in childhood illness. Never mind that it's been 3 years since lockdowns, some places never even closed schools, and lots of kids affected weren't born yet.

Let's try to think clearly here, shall we? 🧵 Much of the "immunity debt" narrative is a just-so story and a transparently obvious effort to minimize possible effects of COVID, convince people that we're nearly back to normal, and discourage mitigation.

Let's at least try to make it a testable scientific hypothesis.
Dec 27, 2023 • 15 tweets • 3 min read
🧵

There are 7 human coronaviruses (so far).

Four of them cause the "common cold" (229E, NL63, OC43, HKU1).

The three most recent are deadly (SARS-CoV, MERS-CoV, SARS-CoV-2).

All three of the deadly ones use the ACE2 receptor. Only one of the common cold viruses (NL63) does. We have never in the history of our species encountered a situation anything like this one, with a coronavirus that is infecting *billions* of hosts, year-round, repeatedly up to several times per year, and being transported all over the world through mass global travel.
Dec 18, 2023 • 10 tweets • 2 min read
"Who cares about variants, I'm taking full precautions" is easily the worst COVID-conscious take I've seen in a long time. Tracking variants is one of the big reasons for doing wastewater surveillance. No wastewater testing, basically no info on COVID rates since most other testing is non-existent.
Dec 17, 2023 • 4 tweets • 1 min read
Narratives that are false and need to finally be rejected:

1. COVID is no worse than flu.
2. Viruses always evolve to become benign.
3. Long COVID is rare.
4. Vax and relax will work.
5. Just a few more infections and we'll have robust hybrid immunity. Narratives that are false and need to finally be rejected, cont'd:

6. It's all "Omicron".
7. It's not airborne.
8. Immunity debt from lockdowns 3 years ago explains everything.
9. Each reinfection gets milder / less likely to result in long COVID.
Dec 15, 2023 • 21 tweets • 5 min read
Here's a good example of how the predictions of "immunity debt" could be properly articulated and tested, using flu in Japan as a case study. 🧵 My brother and his family live in Japan, and my nephews' class is currently closed due to a flu outbreak. The media, of course, attribute this to "immunity debt" as flu cases were way down as a result of COVID mitigation measures. So now it's just catching up, it is argued.
Dec 13, 2023 • 9 tweets • 2 min read
You know me, I like to work through lists of possible explanations for stuff. We're seeing a huge surge in COVID wastewater signal in several places, are there are several possible (non-mutually-exclusive) explanations for it that are worth contemplating. 🧵 Why so much COVID in wastewater? Several non-mutually-exclusive possibilities: 1. More cases, 2. More virus per case in general, 3. More virus in the gut specifically, 4. Longer-lasting infections.
Dec 8, 2023 • 20 tweets • 4 min read
Two terms that I think are used too loosely are "immunity debt/gap" and "immune dysfunction". The strongest, all-or-nothing, just-so story versions of both are problematic. 🧵 "Immunity debt" is a new term (since 2021) that, in one sense simply refers to the well-known and obvious population-level phenomenon by which there come to be more susceptible hosts after a period of low infection and/or vaccination.
Nov 29, 2023 • 7 tweets • 1 min read
I reserve the right to be horrified by the death, suffering, grief, fear, or abuse of any humans regardless of nationality, faith, language spoken, sex, gender, sexual orientation, skin colour, age, socioeconomic status, disabilities, or any other factor that is used to divide. I reserve the right to criticize the words, policies, actions, or inactions of political leaders at any level of government in any part of the world, without this being misconstrued as an attack aimed at the people of any group, geographical region, or nation.