Spyros Lytras
@spyroslytras.bsky.social
Head of the Antigen Evolution and Design lab @antigenevo.bsky.social at Institut Pasteur 🇫🇷 💻🦠🏳️🌈
AlphaFold Database is expanding into pandemic preparedness. Together with NVIDIA, DeepMind, EBI et al. we exhaustively predicted ~1.7 million homo- & heterodimers across 2,812 viral proteomes, resulting in 8,028 high-confidence predictions. 📄 research.nvidia.com/labs/dbr/ass... 🌐 alphafold.ebi.ac.uk
BFVD v3 contains 5.8M viral protein structures, 16× more than v2; 75% high quality, filling a major gap in AFDB coverage. It fully covers 72.6% of reference proteomes and spans 72.7% of ICTV species. Great work by @eunbelivable.bsky.social et al. 📄 www.biorxiv.org/content/10.6... 🌐 bfvd.foldseek.com
Interested in using genomics, big data and AI to tackle future pandemic threats? The @cvrinfo.bsky.social is recruiting two PhD students through the DETECTIVE Doctoral Network 🦠🕵️♂️ shorturl.at/iLrfP
New preprint! We show that poxvirus gene repertoires are shaped by expansion-biased birth-and-death dynamics and genome architectural constraints. Led by Arnon Plianchaisuk (@chainorato) in our lab. Please share! (1/10) www.biorxiv.org/content/10.6...
Thrilled to share our latest preprint on the #evolution of gene repertoires in #poxvirus, a group of giant DNA viruses of medical importance! 🦠🧬 #smallpox #mpox Check out the thread below for a summary of our key findings 👇
Jumpei Ito@jampei2.bsky.social · last mo.New preprint! We show that poxvirus gene repertoires are shaped by expansion-biased birth-and-death dynamics and genome architectural constraints. Led by Arnon Plianchaisuk (@chainorato) in our lab. Please share! (1/10) www.biorxiv.org/content/10.6...
The CGMLab is seeking an experienced postdoctoral researcher to work on an EU project focusing on the bioprospecting of novel microbial enzymes and pathways through metagenomics. Further information and application form can be found at: jobs.cgmlab.org/o/postdoc-po...
Postdoc position - Metagenomic mining & Bioprospecting of novel …
The Comparative Genomics & Metagenomics Lab (CGMLab, https://cgmlab.org) at the Centre for Plant Biotechnology and Genomics (CBGP, Madrid) is seeking a postdoc…
jobs.cgmlab.org
Come work on exciting AI for biology projects in Paris!! 🇫🇷 Details and application below, deadline sept 1st!
Antigen Evolution & Design Lab@antigenevo.bsky.social · 3mo ago🚨 JOB ALERT🚨 We are very excited to be hiring the lab's ✨very first postdoc✨! Work on new AI technologies for decoding antigen protein evolution in a fresh research environment, at the heart of Paris 🇫🇷 Details & link to apply: research.pasteur.fr/en/job/postd... Deadline: Sep 1st
1/ Excited to share our JVI review article with Sanni Översti, @shusukekawakubo.bsky.social, Jumpei Ito, and @antigenevo.bsky.social! From sites to structure to serology: a roadmap for structure-aware molecular evolution of antigenically evolving viruses journals.asm.org/doi/10.1128/...
From sites to structure to serology: a roadmap for structure-aware molecular evolution of antigenically evolving viruses | Journal of Virology
Advances in virus genomics have made it increasingly possible to track evolutionary changes at the population level over the timescales of outbreaks and epidemics (1). Before the current era of large-...
journals.asm.org
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...
Reconstructing the viral histories of human, simian and prosimian immunodeficiency viruses across multiple evolutionary timescales
Abstract. The evolutionary history of simian and prosimian immunodeficiency viruses (SIVs and pSIVs) remains difficult to resolve, because divergence-time
royalsocietypublishing.org
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.
Aris Katzourakis@ariskatzourakis.bsky.social · 3mo agoCompleted 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...
New review out! At @annualreviews.bsky.social for Virology! Check out the summary thread below 👇👇👇
Antigen Evolution & Design Lab@antigenevo.bsky.social · 3mo agoFirst paper with the lab's affiliation!! ✨✨ summarising some of the cool concepts that the Antigen Evolution & Design Lab will be working on! Together with amazing collaborators @mghafari.bsky.social and @grovearmada.bsky.social www.annualreviews.org/content/jour...
Lab account is official! go follow @antigenevo.bsky.social 👇👇👇 research.pasteur.fr/en/team/anti...
Antigen Evolution & Design - Research
Most pathogens have proteins on their surface which are recognised by our immune system and prime it to make antibodies that protect us from future infection. Vaccines contain these proteins to activa...
research.pasteur.fr
Antigen Evolution & Design Lab@antigenevo.bsky.social · 3mo agoInaugural post! We are a brand new lab @pasteur.fr studying how pathogen antigens evolve and how we can exploit these proteins' evolution to make better vaccines! Read a few words from the currently sole member of the lab @spyroslytras.bsky.social below! 😁 www.pasteur.fr/en/research-...
🔬 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-...
Predicting viral evolution with AI
Spyros Lytras is one of four young scientists selected in 2025 to lead new research groups at the Institut Pasteur. He has headed the “Antigen Evolution & Design laboratory” 5-year Group (G5) since Ju...
pasteur.fr
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
Concepts of RNA virus evolution for the design of better antiviral countermeasures
Nature Reviews Microbiology, Published online: 14 May 2026; doi:10.1038/s41579-026-01316-9In this Review, Tran and Vignuzzi examine how molecular processes and evolutionary pressures shape RNA virus diversity and adaptation. They outline how genome structure, mutational pathways and viral interactions influence evolutionary outcomes, offering insights relevant to the design of better vaccines and antiviral strategies.
dlvr.it
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
Spyros Lytras@spyroslytras.bsky.social · 5mo agoSuper 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
People have got to wake up to how bad the situation in US science is right now
Science Magazine@science.org · 5mo agoBreaking news: Indiana University plant microbiologist Roger Innes has been locked out of his laboratory by the school in response to a request by one of his federal funders. The move comes after Innes complained about the government’s prosecution of Chinese postdocs. https://scim.ag/4tsDqRr
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
Complete sequence of Orthohantavirus andesense virus: Swiss resident 2026
Thank you for sharing! Had some free time and had a go at making some segment trees. Brief methods: Downloaded all taxid 1980456 nucleotide sequences Separated by segment and made some preliminary ...
virological.org
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...
Virological characteristics of SARS-CoV-2-related coronaviruses dynamically circulating in Southeast Asia
A study by the G2P-Asia consortium provides a comprehensive analysis spanning fieldwork, as well as experimental and computational investigations into the biology, evolution, and ecology of novel SARS...
cell.com
IQ-TREE 3: Phylogenomic Inference Software using Complex Evolutionary Models academic.oup.com/mbe/article/...
IQ-TREE 3: Phylogenomic Inference Software using Complex Evolutionary Models
Abstract. IQ-TREE (https://iqtree.github.io/) is a widely used open-source software tool for efficiently inferring phylogenetic trees under maximum likelih
academic.oup.com
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...
Virological characteristics of SARS-CoV-2-related coronaviruses dynamically circulating in Southeast Asia
A study by the G2P-Asia consortium provides a comprehensive analysis spanning fieldwork, as well as experimental and computational investigations into the biology, evolution, and ecology of novel SARS...
cell.com
🦠 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/...
