We see very clearly on this graph the incredible acceleration of the substitution rate, with the swarm or cloud JN.1
2) As a reminder, the substitution rates (and not mutation as I had wrongly indicated in my previous post, thx to @AltenbergLee) were:
โถ๏ธ 2020 : 23
โถ๏ธ 2021 : 23.3
โถ๏ธ 2022 : 29
โถ๏ธ 2023 : 29.6
and since the beginning of 2024 : 31.3
3) Also, as very rightly indicated by @_ppmv, it is this level of divergence which is impressive.
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"
5) Pathogens and infectious diseases are not an exception and their diffusion is also accelerating as with socioeconomic indicators.
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 indicated๐) 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.
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 ...
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.
๐๐ผ๐๐-๐พ๐๐-2 ๐๐๐๐๐๐๐๐๐,
๐๐๐ฉ๐ฌ๐๐๐ฃ ๐๐๐พ๐๐๐๐ ๐๐ฃ๐ ๐๐๐ผ๐๐๐๐
(3rd and last part)
In this very interesting study ๐ published in 2024, they explores the eco-evolutionary dynamics between rapidly evolving pathogens, like influenza and SARS-CoV-2 ...
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
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 ...
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 ...
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/10.110โฆ
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 ...
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 !
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."
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
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/10.110โฆ
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 ...
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 ?
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 ...