Share this page!

Enter URL or ID to Unroll

You can paste full URL like: https://x.com/threadreaderapp/status/1644127596119195649
or just the ID like: 1644127596119195649

How to get URL link on X (Twitter) App

  1. On the Twitter thread, click on or icon on the bottom
  2. Click again on or Share Via icon
  3. Click on Copy Link to Tweet
  4. Paste it above and click "Unroll Thread"!
  5. More info at Twitter Help
T. Ryan Gregory πŸ‡¨πŸ‡¦ Profile picture
@TRyanGregory
Jun 15, 2024 β€’ 9 tweets β€’ 4 min read β€’ Read on X
Scrolly
Is SARS-CoV-2 running out of evolutionary space? Is variant evolution slowing down? Is immune escape unlikely anymore? Let's explore. 🧡
Here are some phylogenies (evolutionary trees) of the major SARS-CoV-2 variant lineages from . One is in radial format, the other unrooted, but they show the same information and are both scaled to divergence (number of mutations). nextstrain.org

Evolutionary tree of SARS-CoV-2 variants, radial format, scaled to divergence. "Omicron" variants are vastly more divergent and diverse than the other variants that received Greek letters in 2021.
Evolutionary tree of SARS-CoV-2 variants, unrooted format, scaled to divergence. "Omicron" variants are vastly more divergent and diverse than the other variants that received Greek letters in 2021.
And here are some plots of mutations over time, again from . There is no sign of this rate of accumulation of mutations slowing down (if anything, more recent variants are above the trend line). nextstrain.org
Mutations over time for SARS-CoV-2 variants.
It's worth looking at spike (S1) mutations specifically. Note two things here:

1) We're still getting a LOT of new mutations.

2) These come in rather discrete jumps, then a flatter plateau. That's because of recombination or within-host evolution in persistent infections. Spike mutations over time for SARS-CoV-2 variants.
Here is some info on immune escape and ACE2 binding -- that is, how well the variant avoids existing antibodies and how well it can attach to the receptors on our cells. The top right is the "uh oh" zone where it is good at both. From . nextstrain.org
Immune escape vs. ACE2 binding compared to BA.2 for SARS-CoV-2 variants. Many of the most recent variants are in the "uh oh zone" with both high immune escape and receptor binding.
Looking at global trends for immune escape and ACE2 binding for the last 20 days, we see lots of variants with very high immune escape compared to BA.2, and some that also have high ACE2 binding. Note the change between BA.2.86 (circled) and its descendants. From @RajlabN. Immune escape vs. ACE2 binding compared to BA.2 for the most recent SARS-CoV-2 variants. Both have generally increased between BA.2.86 and its descendants.
Here's immune escape (vs. BA.2) over time, from . Again, the virus is not running out of ways to escape current immunity (which is partial, temporary, and changing according to vaccinations and infections). From . nextstrain.org
nextstrain.org
Immune escape compared to BA.2 over time for SARS-CoV-2 variants. The trend line continues to be highly positive -- that is, immune escape continues to evolve.
Why does this keep happening, contrary to minimizer assumptions? Because:

1) Orgel's second rule: "Evolution is cleverer than you are".

2) This: More infections means more variant evolution.
A reminder about Greek letters and the decision to keep calling everything "Omicron".

β€’ β€’ β€’

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

Keep Current with T. Ryan Gregory πŸ‡¨πŸ‡¦

T. Ryan Gregory πŸ‡¨πŸ‡¦ 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

T. Ryan Gregory πŸ‡¨πŸ‡¦ Profile picture
Jun 12
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
T. Ryan Gregory πŸ‡¨πŸ‡¦ Profile picture
Jun 6
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
T. Ryan Gregory πŸ‡¨πŸ‡¦ Profile picture
May 27
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
T. Ryan Gregory πŸ‡¨πŸ‡¦ Profile picture
Apr 29
Btw folks, what happened is that QuΓ©bec saved us all from Poilievre. Bloc voters went Liberal this time to keep him out.

Ontario, not so much. Big gains for the Cons.

BC was where the NDP did best last election, and this time it went Lib and Con.
So, we essentially traded a Liberal minority with progressive parties being very influential to a Liberal minority with a huge Conservative opposition and minimal progressive representation.

The fact that 41.4% voted Con (vs. 43.5% Lib) isn't a good sign either.
Yes, I'm relieved that it's not Poilievre as PM and I'm glad he lost his seat. But beyond that, we're not in a very good place overall. The major rightward shift isn't going to be good, especially when the Liberals eventually lose to the Conservatives.
Read 4 tweets
T. Ryan Gregory πŸ‡¨πŸ‡¦ Profile picture
Apr 1
It's very important to be clear about what is happening in the Canadian election and how progressives need to approach it. 🧡

The LPC surge toward a majority is due primarily to a collapse of support for the NDP and Bloc, and much less so a drop in support for the CPC.

1/ Vote and seat projections for Canada.
Vote and seat projections for Ontario.
Vote and seat projections for QuΓ©bec.
This means that the Libs are mostly picking up progressive voters who are planning to vote strategically to stop the Cons. They are not picking up huge numbers of "moderate conservatives".

Cons support is generally committed but Libs support isn't.



2/angusreid.org/canadian-elect…
The *winning strategy* for Libs is to make strategic voting by progressives as painless as possible by leaning *leftward*.

The winning approach for progressive voters is to make it clear they cannot be taken for granted and do not agree with rightward drift.

3/
Read 6 tweets
T. Ryan Gregory πŸ‡¨πŸ‡¦ Profile picture
Mar 19
Thoughts on pandemics, inclusion, annexation, Indigenous issues, climate, genocide, and more and the connections I see among them. I fully acknowledge that I am writing this from a position of substantial intersectional privilege.

🧡

1/
I really hoped that the (ongoing) SARS-CoV-2 pandemic would inspire us to make meaningful, positive changes in society. Indeed, early on it seemed like privileged people finally understood what it was like to lack access to things we otherwise take for granted.

2/
Sadly, but perhaps predictably, we instead rushed back to the status quo as quickly as we could. If anything, things are worse now in terms of public health, accessibility and inclusion, and global health equity. Infectious disease has been actively normalized.

3/
Read 10 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!

Send Email!

:(