Completed our work on reconstructing the viral histories of human, simian and prosimian immunodeficiency viruses across multiple evolutionary timescales, with @mghafari.bsky.social & @psimmond.bsky.social royalsocietypublishing.org/rspb/article...

A long time in the making, and exciting to finally see this work published. We show how the PoW model resolves evolutionary events across vastly different timescales, from the origins of HIV-1 and HIV-2 lineages, through the deeper history of SIVs, to the ancient split between SIV and pSIV and more.

New review out! At @annualreviews.bsky.social for Virology! Check out the summary thread below 👇👇👇

Lab account is official! go follow @antigenevo.bsky.social 👇👇👇 research.pasteur.fr/en/team/anti...

🔬 Meet Spyros Lytras, one of our new G5 group leaders! Using AI to predict viral protein evolution, he's designing vaccines for strains that don't yet exist. No more waiting for threats to emerge—be ready ahead of time. The future of pandemic preparedness. 🧬 📖 www.pasteur.fr/en/research-...

A very busy but exciting first week at @pasteur.fr !! Got a nice empty office that will hopefully start filling up soon! 😁😁

📣📣Very pleased to welcome @spyroslytras.bsky.social to our department @ipdbsc.bsky.social @pasteuredu.bsky.social 👇

New online! Concepts of RNA virus evolution for the design of better antiviral countermeasures

Nextstrain #ANDV trees updated with a few improvements: - 2 outbreaks marked - host scientific/common name added - province now visible on map - date colouring added Here's a quick tour of how to change colours, geography & names! Links to trees here (scroll down): nextstrain.org/groups/hodcr...

With Eugene Koonin, we wrote a rather comprehensive review on the origin, evolution and organization of the #virosphere. We describe all 10 viral realms and the logic behind them, and so much more. Check it out! comptes-rendus.academie-sciences.fr/biologies/ar...

some updates and small corrections on the hantavirus phylogeny below: virological.org/t/complete-s... the cruise ship virus is from ANDV Clade 3 (see Fig2A journals.asm.org/doi/10.1128/...) Clade 3 has confirmed human cases, Clade 2 has confirmed H2H, safe to assume both can H2H #ANDV

People have got to wake up to how bad the situation in US science is right now

I've built some initial Nextstrain phylogenies of the Andes Hantavirus variant, which include the sequence generated by HUG & UniZurich, Switzerland. Please interpret with caution. By segment: S: nextstrain.org/groups/hodcr... M: nextstrain.org/groups/hodcr... L: nextstrain.org/groups/hodcr...

Super quick sequencing from the Swiss team!! I found some time to do a quick phylo analysis posted here: virological.org/t/complete-s... #hantavirus #ANDV

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Diversity of SARS-CoV-2-related coronaviruses dynamically co-circulating in Southeast Asia & their virological characteristics relative to SARS-CoV-2 @cellcellpress.bsky.social @systemsvirology.bsky.social www.cell.com/cell/fulltex...

BREAKING🔔 The 57th paper from G2P-Japan🇯🇵 is out at Cell @cellcellpress.bsky.social 🦇!! We elucidated the virological characteristics of a new bat coronavirus identified in Thailand🇹🇭 The debut work by G2P-Asia🌏! Please repost🔥 www.cell.com/cell/fulltex...

IQ-TREE 3: Phylogenomic Inference Software using Complex Evolutionary Models academic.oup.com/mbe/article/...

Been a while since a new SARS-CoV-2 relative came up... here's a new one! 🦇🦇 Together with Dr. Wacharapluesadee's team at Chulalongkorn we comprehensively describe a new sarbecovirus clade from Thailand! Now out in @cp-cell.bsky.social @systemsvirology.bsky.social www.cell.com/cell/fulltex...

🦠 NEW | Fully funded PhDs in #virology We are excited to offer three fantastic opportunities to do joint PhDs between @cvrinfo.bsky.social and @pirbrightinst.bsky.social. Funded for UK home students. Deadline for applications: Fri 8 May 26 Links and details below ⬇️

Protein Language Models (PLMs) could transform outbreak response New research from @kieranlamb.bsky.social & colleagues show that PLMs can identify mutation hotspots and key features of viral proteins - even from a single sequence. www.gla.ac.uk/research/az/...

3rd human #H5N1 case of 2026 in #Cambodia A 3-year-old boy from Oddar Meanchey province, currently hospitalized and receiving treatment. 🔬🧪😷🐓🦠🥼💉 2026: 3 cases, 0 deaths Since 2023: 37 cases, 15 deaths (CFR 40.5%) Since 2004: 93 cases, 52 deaths (CFR 55.9%)

From @systemsvirology.bsky.social Experimental SARS-CoV-2 infection of Rhinolophus ferrumequinum www.biorxiv.org/content/10.6... 🎶 another one bites the dust 🎶

Lab Leakers: "SARS-CoV-2 can't infect bats, so it must have been made in a lab". Science: "Let's do the experiment". SARS-CoV-2 behaves exactly like one would expect in a reservoir species - low-level infection, no overt disease, etc. Elegant study from Sato Lab: www.biorxiv.org/content/10.6...

We are delighted to announce that our new website is now live! Check it out: www.cvr.ac.uk

Want to work on viral community ecology and virus genomics? 🔎 🧬 🦠 Come and work with us at RVC! Applications for a 0.5 FTE lab technician role now open, suitable for someone with lab experience and a relevant BSc/MSc. jobs.rvc.ac.uk/Vacancy.aspx...

Very cool work! Really pinning down some important hypotheses about virus emergence! got myself a comment in the nyt article (although @davidlrobertson.bsky.social had the best quote! 👀) Archived article link here: archive.md/UjxJ0

There's a common misconception that zoonotic viruses require significant adaptation to jump from animals to cause human epidemics. Not so 👇. Further, we see clear signs of 1977 flu experiencing cell passage, prior to epidemic. SARS-CoV-2? Business as usual. www.sciencedirect.com/science/arti...

In new study led by Brendan Larsen, we map functional constraint across the Nipah virus F protein to define constrained epitopes for antibody targeting and identify mutations that stabilize the prefusion conformation for vaccine immunogens. www.pnas.org/doi/10.1073/...

We have an open Assistant Professor position (tenure track) @ethz.ch in Computational Immunology - ethz.ch/en/the-eth-z... Please apply / share!

It is almost five years since I first applied AlphaFold to a handful of viral proteins. Today, hundreds of thousands of predictions and many discoveries later, we are delighted to announce the integration of our Viro3D dataset into the @ebi.embl.org and Google DeepMind AlphaFold Database.

What a great conference!! Leaving Brisbane inspired about the future of structural phylogenetics! Thanks again to the organisers @cpuentelelievre.bsky.social @proteinmechanic.bsky.social and Jordan Douglas for an amazing work putting it all together!

Very excited to be in (slightly rainy until tomorrow ☔) Brisbane attending the first Australasian Protein Structural Phylogenetics Meeting #strphy26 @strphy.bsky.social Catch me at my talk tomorrow afternoon or at welcome drinks tonight! 🥂

First human #H5N1 case of 2026 in #Cambodia: a 30-year-old man from Kampot province. Sequencing, virus isolation & animal investigations ongoing. Dead chicken at home before onset. Patient has since recovered. 🦠💉😷🐓🥼🔬🧪 Sequencing, contact tracing, and poultry investigations ongoing.

Our paper on inferring context dependent entropy using protein language models is officially out in NAR Genomics & Bioinformatics! 🧬🤖 with Adam Strange, Jumpei Ito, and @systemsvirology.bsky.social academic.oup.com/nargab/artic... details below... #NARGAB

FoldMason is out now in @science.org. It generates accurate multiple structure alignments for thousands of protein structures in seconds. Great work by Cameron L. M. Gilchrist and @milot.bsky.social. 📄 www.science.org/doi/10.1126/... 🌐 search.foldseek.com/foldmason 💾 github.com/steineggerla...

Remember? RNA virus journal club is already this Thursday! 🤩 Join us and join our (RdRp summit) slack (link in the comment): calendar.app.google/K2fwcsL78K1E... RNA Virus Journal ClubJoin Zoom Meeting us02web.zoom.us/j/8109697228... Meeting ID: 810 9697 2281 Passcode: 174610

Great opportunity to learn how to make very cool looking phylogenies by a real tree wizard @evogytis.bsky.social ! 🌲🧙‍♂️ Don't miss out!

🎉 Congratulations to Dr Daniel Weir for recently passing his Viva! Daniels research explored how influenza A virus infection moves directly between cells, independently of virus particles, focusing on how infection induces the formation of tunnelling nanotube-like structures.

New preprint led by our MSc student Wenye Li!! 🎉 @systemsvirology.bsky.social What we find is a historic genetic interplay between sarbecoviruses and their horseshoe bat hosts' ACE2 receptor! 🦇 🧵... www.biorxiv.org/content/10.1...

🦠🧪🧬🚨 New paper and database alert: the new IMG/VR release is now MetaVR ! We have a new website - meta-virome.org - with quick search capabilities for the >24M viruses, >12M vOTUs, and >42M protein clusters (including >790k with predicted structures !). academic.oup.com/nar/advance-...

Big congrats to Matt Turnbull @samjwilsonphd.bsky.social and all co-authors!! 🎉🎉 New paper in @science.org showing how the interaction between flu PB1 and host ANP32A control how flu can replicate in higher body temperatures! 🦆🦆🦆 www.science.org/doi/10.1126/...

Amazing example of influenza cheat/cooperator cycles in this recent paper - the repeatability of the oscillatory cycles is so striking Congrats to @alnajifg.bsky.social , @christopherbrooke.bsky.social , @vignuzzilab.bsky.social & friends www.biorxiv.org/content/10.1... 🧪 #socialviruses

Great to be teaching about structural predictions and metagenomic discovery of diverse viruses at @virus-metagenomics.bsky.social ! And even greater to be visiting sunny Stellenbosch! ☀️☀️

Guess the news is officially out! Extremely excited to announce that I will be starting my own laboratory at Institut Pasteur @pasteur.fr this coming spring! Slight change to my office window view from Tokyo Tower🗼 to the Tour Eiffel. 🇫🇷

Great to have you over Mahan!!! 😁😁😁 A very fun trip and the start of some exciting science collabs soon! 👀👀

New paper out in iScience @cellpress.bsky.social We show that #sand_fly biting reprograms skin fibroblasts, making them more permissive to virus infection => #fibroblasts aren’t bystanders, they help define severity/clinical outcome to infection AND #vector biting is key 👉 doi.org/10.1016/j.is...

New preprint alert!! 🚨🚨🚨in collaboration with the Letko @fviromics.bsky.social and Baric labs! Just in case you're tired of sarbecoviruses, this time we looked at ACE2-using merbecoviruses! specifically the first HKU5r-CoVs detected in mink a couple of years ago. www.biorxiv.org/content/10.1...

🎉 Fletcher lab PhD student Emma Davies reflecting on her prize winning talk - we’re super proud of you Emma - many congrats! 🎉 @cvrinfo.bsky.social @uofgsii.bsky.social @uofgmvls.bsky.social