Emmanuel Profile picture
Jun 6 โ€ข 8 tweets โ€ข 4 min read โ€ข Read on X
๐™๐™ƒ๐™€ ๐˜ผ๐˜พ๐˜พ๐™€๐™‡๐™€๐™๐˜ผ๐™๐™„๐™Š๐™‰ ๐™ค๐™› ๐™ƒ๐™„๐™Ž๐™๐™Š๐™๐™”

We see very clearly on this graph the incredible acceleration of the substitution rate, with the swarm or cloud JN.1 Image
2) As a reminder, the substitution rates (and not mutation as I had wrongly indicated in my previous post, thx to @AltenbergLee) were:
โ–ถ๏ธ 2020 : 23
โ–ถ๏ธ 2021 : 23.3
โ–ถ๏ธ 2022 : 29
โ–ถ๏ธ 2023 : 29.6
and since the beginning of 2024 : 31.3


Image
Image
Image
Image
3) Also, as very rightly indicated by @_ppmv, it is this level of divergence which is impressive. Image
4) The title of my post comes from the famous book by Gerard Piel. Sometimes people talk about this subject using the terms of "The Great Acceleration"
Image
Image
5) Pathogens and infectious diseases are not an exception and their diffusion is also accelerating as with socioeconomic indicators. Image
6) We only regret that with each new variant / major mutation (Flirt, KP.2, KP.3 or LB.1 and KP.2.3 as my friend Kei Sato @SystemsVirology has just indicated๐Ÿ‘‡) some people feel obliged to announce the emergence of a new wave.
7) In our opinion, there is a misunderstanding of the concept of "fertile mutation". For a new wave to emerge, it is not enough for in vitro studies to show its capacity of immune escape, it must also be able to encounter favorable terrain (immune landscape).
8) To conclude, during our previous post on this subject 6 months ago, @flodebarre sent us this remarkable study which we recommend.


Thanks for reading ๐Ÿ™ academic.oup.com/ve/article/8/2โ€ฆ
Image

โ€ข โ€ข โ€ข

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

Keep Current with Emmanuel

Emmanuel 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 @ejustin46

Jun 8
๐™๐™‰๐™Ž๐™๐™Š๐™‹๐™‹๐˜ผ๐˜ฝ๐™‡๐™€!
๐™Ž๐˜ผ๐™๐™Ž-๐˜พ๐™Š๐™‘-2, ๐™„๐™ฃ๐™›๐™ก๐™ช๐™š๐™ฃ๐™ฏ๐™– ๐˜ผ, ๐™„๐™ฃ๐™›๐™ก๐™ช๐™š๐™ฃ๐™ฏ๐™– ๐˜ฝ, ๐™๐™ช๐™ข๐™–๐™ฃ ๐™ง๐™š๐™จ๐™ฅ๐™ž๐™ง๐™–๐™ฉ๐™ค๐™ง๐™ฎ ๐™จ๐™ฎ๐™ฃ๐™˜๐™ฎ๐™ฉ๐™ž๐™–๐™ก ๐™ซ๐™ž๐™ง๐™ช๐™จ, ...

respiratory-research.biomedcentral.com/articles/10.11โ€ฆ
2) This study assessed the performance of a multiplex respiratory panel detecting SARS-CoV-2, influenza A/B, and respiratory syncytial virus (RSV) in two time periods. In early 2022, SARS-CoV-2 infections dominated (66.1%), but influenza A (1.6%), RSV (0.7%), and ... Image
3) ...influenza B (0.1%) were also detected. In the 2022/23 season, SARS-CoV-2 positivity decreased to 9.6%, while influenza A (3.5%), RSV (2.8%), and influenza B (0.6%) increased. Co-detections remained around 1-2% across both periods. Image
Read 4 tweets
Jun 8
๐™Ž๐˜ผ๐™๐™Ž-๐˜พ๐™Š๐™‘-2 ๐™€๐™‘๐™Š๐™‡๐™๐™๐™„๐™Š๐™‰,
๐™—๐™š๐™ฉ๐™ฌ๐™š๐™š๐™ฃ ๐™๐™„๐˜พ๐™๐™„๐™Š๐™‰ ๐™–๐™ฃ๐™™ ๐™๐™€๐˜ผ๐™‡๐™„๐™๐™”
(3rd and last part)

In this very interesting study ๐Ÿ‘ published in 2024, they explores the eco-evolutionary dynamics between rapidly evolving pathogens, like influenza and SARS-CoV-2 ... Image
2) ...and the immune responses of their hosts.ย 

As pathogens spread, host immunity builds up, creating selective pressures that drive the pathogens to rapidly evolve immune-evading variants. arxiv.org/abs/2402.07252
Image
3) However, host immunity also adapts, limiting the growth advantage of new variants. They use a (SIR) model to simulate this co-evolutionary process, showing that depending on factors like cross-immunity between strains and durability of immune responses ... Image
Read 8 tweets
Jun 8
๐™Ž๐˜ผ๐™๐™Ž-๐˜พ๐™Š๐™‘-2 ๐™€๐™‘๐™Š๐™‡๐™๐™๐™„๐™Š๐™‰,
๐™—๐™š๐™ฉ๐™ฌ๐™š๐™š๐™ฃ ๐™๐™„๐˜พ๐™๐™„๐™Š๐™‰ ๐™–๐™ฃ๐™™ ๐™๐™€๐˜ผ๐™‡๐™„๐™๐™”
(2nd part)

In another study with @jbloom_lab , they showed that the Omicron mutation spectrum is more similar to the long-term evolutionary spectrum of other sarbecoviruses ... Image
2) ...hinting that SARS-CoV-2 may be trending back towards a bat-like mutation profile after adapting to humans.

In this study, examining changes in the mutational spectrum of SARS-CoV-2 over time, they focused on the relative rates of ... biorxiv.org/content/10.110โ€ฆ
Image
3) ... different single nucleotide mutations at four-fold degenerate sites (where mutations are expected to be neutral). They found clear shifts in the mutation spectrum across different SARS-CoV-2 clades, with the most striking change being a ~2-fold decrease ... Image
Read 6 tweets
Jun 8
๐™Ž๐˜ผ๐™๐™Ž-๐˜พ๐™Š๐™‘-2 ๐™€๐™‘๐™Š๐™‡๐™๐™๐™„๐™Š๐™‰,
๐™—๐™š๐™ฉ๐™ฌ๐™š๐™š๐™ฃ ๐™๐™„๐˜พ๐™๐™„๐™Š๐™‰ ๐™–๐™ฃ๐™™ ๐™๐™€๐˜ผ๐™‡๐™„๐™๐™”
(1st part)

An example to start.
BA.2.86, the "father" of the JN.1*, was presented as THE VARIANT which suddenly emerged at the end of 2023. However, BA.2.86 had existed since early 2022 ! Image
2) Alex Sigal @sigallab explained it perfectly, in a post from September 8, 2023, with a variant which has gradually gained its "mutations without spreading because it was either a long infection in someone immunosuppressed or in an animal reservoir."
Image
Image
3) Far from the fictions, which are there above all to make noise, there is a virus which is evolving in an interesting way, and we would like to approach this subject, drawing in particular on the remarkable work of Richard Neher @richardneher
Read 9 tweets
Jun 7
๐™ˆ๐™ค๐™™๐™š๐™ก๐™ž๐™ฃ๐™œ ๐™ฅ๐™ค๐™ฅ๐™ช๐™ก๐™–๐™ฉ๐™ž๐™ค๐™ฃ ๐™ข๐™ค๐™ซ๐™š๐™ข๐™š๐™ฃ๐™ฉ๐™จ ๐™›๐™ค๐™ง ๐™ช๐™ฃ๐™™๐™š๐™ง๐™จ๐™ฉ๐™–๐™ฃ๐™™๐™ž๐™ฃ๐™œ ๐˜พ๐™Š๐™‘๐™„๐˜ฟ-19 ๐™™๐™ฎ๐™ฃ๐™–๐™ข๐™ž๐™˜๐™จ

Forgive me for the lightness of the statement but "a virus has no legs".
It is its hosts that allow its transmission.
medrxiv.org/content/10.110โ€ฆ
Image
2) In this study, they developed a metapopulation SEIR model to simulate COVID-19 transmission across the North American region, including Canada, the United States, and Mexico.
The model-inference system uses the Ensemble Adjustment Kalman Filter to estimate time-varying ... Image
3) ...transmission rates, ascertainment rates, and reproductive numbers for each location based on reported case data. The results highlight important differences in COVID-19 dynamics among the three countries.

Why modeling population movements is so important ? Image
Read 9 tweets
Jun 7
๐™ƒ๐™ž๐™œ๐™ ๐™ก๐™š๐™ซ๐™š๐™ก ๐™ค๐™› ๐™ฃ๐™š๐™ช๐™ฉ๐™ง๐™–๐™ก๐™ž๐™ฏ๐™ž๐™ฃ๐™œ ๐™–๐™ฃ๐™ฉ๐™ž๐™—๐™ค๐™™๐™ž๐™š๐™จ = ๐™๐™ž๐™œ๐™ ๐™ก๐™š๐™ซ๐™š๐™ก ๐™ค๐™› ๐™ฅ๐™ง๐™ค๐™ฉ๐™š๐™˜๐™ฉ๐™ž๐™ค๐™ฃ ๐™–๐™œ๐™–๐™ž๐™ฃ๐™จ๐™ฉ ๐™ž๐™ฃ๐™›๐™š๐™˜๐™ฉ๐™ž๐™ค๐™ฃ

๐™’๐™๐™–๐™ฉ, ๐™ž๐™› ๐™ž๐™ฉ ๐™ฌ๐™–๐™จ๐™ฃ'๐™ฉ ๐™ฉ๐™๐™–๐™ฉ ๐™จ๐™ž๐™ข๐™ฅ๐™ก๐™š?
wwwnc.cdc.gov/eid/article/29โ€ฆ
Image
2) Several studies have shown that higher levels of neutralizing antibodies are associated with immune protection from symptomatic SARS-CoV-2 infection. However, the estimated relationship between neutralizing antibody levels and protection has varied between studies.
3) The authors reconciled these differences by normalizing the antibody titers across studies. They found that the study results converge on a consistent relationship between antibody levels and protection from COVID-19. This can be useful for planning future vaccine use ... Image
Read 8 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!

:(