T. Ryan Gregory 🇨🇦 Profile picture
Mar 28, 2023 7 tweets 2 min read Read on X
Don't learn your human evolution from virology textbooks. We did *not* evolve alongside highly transmissible respiratory viruses in densely crowded indoor spaces for millions of years. You're thinking of bats in caves.

1/
These are *very* new for us as an evolutionary lineage (mostly post-agriculture 13,000 years ago, some within the past few hundred years or even decades).

* Being in contact with domesticated livestock
* Encroaching on wildlife habitat in large numbers

2/
* Living in huge population densities
* Coming into contact with huge numbers of other people, with a ton of intermixing all the time
* Living to old age
* Spending most of our time indoors
* Travelling around the world

3/
There's a reason bats are a major source of zoonotic viruses. That can live with them, which is possible because they *do* have immune adaptations to tolerate regular infections, because they *did* evolve under those conditions.

nature.com/articles/s4158…

• • •

Missing some Tweet in this thread? You can try to force a refresh
 

Keep Current with T. Ryan Gregory 🇨🇦

T. Ryan Gregory 🇨🇦 Profile picture

Stay in touch and get notified when new unrolls are available from this author!

Read all threads

This Thread may be Removed Anytime!

PDF

Twitter may remove this content at anytime! Save it as PDF for later use!

Try unrolling a thread yourself!

how to unroll video
  1. Follow @ThreadReaderApp to mention us!

  2. From a Twitter thread mention us with a keyword "unroll"
@threadreaderapp unroll

Practice here first or read more on our help page!

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

Did Thread Reader help you today?

Support us! We are indie developers!


This site is made by just two indie developers on a laptop doing marketing, support and development! Read more about the story.

Become a Premium Member ($3/month or $30/year) and get exclusive features!

Become Premium

Don't want to be a Premium member but still want to support us?

Make a small donation by buying us coffee ($5) or help with server cost ($10)

Donate via Paypal

Or Donate anonymously using crypto!

Ethereum

0xfe58350B80634f60Fa6Dc149a72b4DFbc17D341E copy

Bitcoin

3ATGMxNzCUFzxpMCHL5sWSt4DVtS8UqXpi copy

Thank you for your support!

Follow Us!

:(