5/ Figure 3 looks at influenza A(H3N2) over longer timescales, using the PLANT method (www.biorxiv.org/content/10.1...) Genetic change keeps accumulating, but antigenic evolution does not simply move in a straight line away from the past. Instead, the antigenic trajectory can loop back.

3/ Across SARS-CoV-2 genomic regions, we highlighted regions with higher inferred mutational fitness, using the Bloom and Neher framework, which also tend to show faster nonsynonymous molecular clock like change measured by Hamming distance.

2/ The core idea is simple: viral genomes tell us what changed, but not always what those changes do. We propose a conceptual roadmap linking sequence variation, phylogenies, protein structure, serology, ML-based prediction, and epidemiological dynamics to understand antigenic evolution.

It was a pleasure to host @systemsvirology.bsky.social at @biology.ox.ac.uk today for a fascinating talk on the origins and phenotypic characteristics of SARS-CoV-2!

Had an absolutely wonderful few days at #JSV72 in Hamamatsu & IMSUT in Tokyo. Huge thanks to @shusukekawakubo.bsky.social, @shigeru0701.bsky.social, @spyroslytras.bsky.social & everyone in the @systemsvirology.bsky.social lab for being such brilliant hosts. Japan has been an amazing experience 🇯🇵✨

🚨Our study on characterising the within-host SARS-CoV-2 evolution during persistent infections is now out in @lancetmicrobe.bsky.social! 👉 www.sciencedirect.com/science/arti...

Looking forward to welcoming you tomorrow, @spyroslytras.bsky.social! Spyros will be giving a seminar in Biology (Mansfield Road) at 11am on ‘AI-enabled structural comparisons uncover the deep evolutionary histories of viral glycoproteins’ — come along if you’re around!

Looking forward to tomorrow’s @smtpb.bsky.social event (5:30–7:00pm UK time)! If you’re interested, you can register here: stanford.zoom.us/meeting/regi...

🚨We’re hiring a Postdoc to join our group at Oxford! We’re developing methods to understand how pathogens evolve—across hosts, over time, & through molecular & structural change. Keen or know someone who is? Please share! 🕒 3-year post 📅 Deadline: 30 May 🔗 Apply: www.jobs.ox.ac.uk/vacancy/179640

Again naively eyeballing this H3N2 tree from Nexstrain, It seems like something funky is happening around 1985. Added lines to show the approximate rates — red seems to be a bit faster. But there doesn't seem to be a jump in distance. So, probably nothing to do with persistents?

I'm not as familiar with the influenza A literature, but is there a known cause for the distinct rate variation observed in hemagglutinin over time? It seems a lot like a step-wise increase, which I might naively attribute to a persistent infection. Could that be the case?

Looking ahead, it'd be exciting to see if we can find more evidence for ancient origins of plant viruses. P.S.: After a few tries, I've come to the conclusion that DALL·E is really not good at making inspiring images of plant viruses!

Lineage replacement and evolution captured by 3 years of the United Kingdom Coronavirus (COVID-19) Infection Survey royalsocietypublishing.org/doi/10.1098/...