T. Ryan Gregory 🇨🇦 Profile picture
Jan 13, 2024 8 tweets 3 min read Read on X
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).
Consider the situation with the 1918 flu pandemic.

In 1918:

* The human population was less than 1/4 as large as it is today.
* There was no global air travel.
* Life expectancy was about 1/2 what it is today.
* Only about 30% of the population was infected.
Very basic evolutionary theory shows that population size matters *a lot*. Larger population of viruses means:

* More mutations added to the gene pool.
* More opportunity for recombination and within-host evolution.
* Stronger natural selection on fit mutations.
With 8 billion potential hosts who can be infected year-round and up to several times per year, that is a lot of virus. Like, a lot a lot. Enough that every possible point mutation is probably happening and being passed on every single day.

pnas.org/doi/10.1073/pn…
Movement of infected hosts all around the world means that a variant that evolves anywhere will soon appear everywhere. With waning immunity and immune escaping variants, this means a high baseline and a lot of area under the curve even without huge peaks.
It's a myth that viruses must evolve to become benign lest they drive hosts extinct. Not when there are billions of hosts available. And it is a perfectly viable outcome to become less virulent acutely but take up residence in organs and do damage long term, after transmission.
The answer is not people getting infected more so that the virus becomes benign or we finally get herd immunity.

The answer is less virus.

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More from @TRyanGregory

Jan 24
I need Canadians to think about what is happening here at home. Carney is cutting the very agencies we need more than ever as things erode in the US.

Wake. Up.

🧵
Read 8 tweets
Dec 5, 2025
Well, it's that time again. Meet "Cicada", BA.3.2* (including descendant RE.*). This one has been underground for years (its ancestor BA.3 hasn't been circulating since early 2022, and didn't do much then either) but is now emerging as a contender for the next major lineage.
Volunteer variant trackers have been watching this one since March, with it popping up around the world throughout November. It's another highly divergent variant (50 spike mutations) that evolved within a chronically infected host.

Read 6 tweets
Oct 5, 2025
There is growing interest in possible links between SARS-CoV-2 and cancer. I strongly recommend this video series with @arijitchakrav which discusses why it might be even worse.

🧵

Part 1:

Part 2:

Part 3:

Read 4 tweets
Jun 12, 2025
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
Jun 6, 2025
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
May 27, 2025
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

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