How can we move beyond reading virus genomes as strings of letters on a phylogenetic tree, and instead place those genetic changes in their biological context? 🧬 A blog by @mghafari.bsky.social discusses new ways of thinking about old problems 🦠👇

From viral histories to protein structures: new directions for understanding virus evolution

bit.ly

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

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 · 4w ago

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...

Very happy to have been part of this work w/ Spyros Lytras and Joe Grove! New structural prediction tools are opening up exciting possibilities for virus discovery and for reconstructing their deep evolutionary histories, as we explore in our new review article www.annualreviews.org/content/jour...

Studying the Deep Evolution of Viruses in the Era of Artificial Intelligence Structure Prediction

High mutation rates erode viral sequence similarity, obscuring deep evolutionary history. While protein structure is far more conserved than sequence, its use in evolutionary studies has historically ...

annualreviews.org

Antigen Evolution & Design Lab@antigenevo.bsky.social · 3w ago

First 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...

First 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...

Studying the Deep Evolution of Viruses in the Era of Artificial Intelligence Structure Prediction

High mutation rates erode viral sequence similarity, obscuring deep evolutionary history. While protein structure is far more conserved than sequence, its use in evolutionary studies has historically ...

annualreviews.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

Inaugural 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-...

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

We’ve posted a preliminary molecular evolutionary analysis of the current Bundibugyo virus disease outbreak in DRC and Uganda, using 10 available BDBV genomes to reconstruct outbreak mutations and explore rate-conditioned tMRCA/growth estimates. virological.org/t/molecular-...

Molecular evolutionary analysis of the current Bundibugyo virus disease outbreak in DRC and Uganda

Authors: Gina Cuomo-Dannenburg and Mahan Ghafari Note on data use This is an informal analysis and is not intended as a formal preprint or manuscript in its current form. The aim of this post is to p...

virological.org

Incredibly valuable and timely work by Lissette, Edyth, and colleagues!

Edyth Parker@edythparker.bsky.social · 2mo ago

Our initial work on the potential geographic and ecological origin of the MV Hondius Andes virus outbreak showing the outbreak lineage clusters most closely with some of our new sequences from southern Chile (lead by the brilliant Lissette): virological.org/t/potential-....

Trying to make sense of the unfolding Hantavirus outbreak from molecular sequence data. Many caveats apply; this is just a post on a blog, not a peer reviewed research paper, but is our attempt to make sense of the data so far and help out. All subject to revision etc.

Mahan Ghafari@mghafari.bsky.social · 3mo ago

Our two-part analysis of the current MV Hondius Andes virus outbreak is now live, including reconstruction of the outbreak molecular clock dating of the closest known ancestors of the outbreak lineage. Part 1: outbreak sequence reconstruction and rooting virological.org/t/molecular-...

Our two-part analysis of the current MV Hondius Andes virus outbreak is now live, including reconstruction of the outbreak molecular clock dating of the closest known ancestors of the outbreak lineage. Part 1: outbreak sequence reconstruction and rooting virological.org/t/molecular-...

Molecular evolutionary analysis of the current MV Hondius Andes virus outbreak

Preliminary reconstruction of the current MV Hondius Andes virus outbreak sequences Note on data use This is an informal analysis of currently available consensus sequences and is not intended as a fo...

virological.org

We're recruiting! We're looking for two graduate students to join us at UBC in Vancouver. Fully funded and open to global applicants, with flexible start-date. Topics include theory, bioinformatics, and microbiology. More details: asherleeks.com/apply #socialviruses #evosky #virosky 🧪

The Social Lives of Viruses is coming to Vancouver, Canada, from 4th-8th August 2026! This is a free meeting dedicated to all aspects of virus-virus interactions & evolution. To apply: socialviruses.zoology.ubc.ca @sociovirology.bsky.social #socialviruses #evosky #lovevirology #virosky

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!

I'm excited to introduce our new workflow for detecting endogenous viral elements - HI-FEVER. 🖥️🧬 academic.oup.com/bioinformati... 🧵 Big thanks to @ariskatzourakis.bsky.social, @humanceae.bsky.social, José Gabriel and Cormac for bringing this from conception to fruition!

HI-FEVER: a Nextflow pipeline for the high-throughput discovery and annotation of endogenous viral elements

AbstractSummary. Endogenous viral elements (EVEs) offer valuable insights into virus and host evolution, but their detection remains computationally and bi

academic.oup.com

Congratulations to @mghafari.bsky.social who has been selected as one of the New Voices in Virology! Mahan's research focuses on the evolution of pathogens, particularly those with epidemic or pandemic potential and with implications for human, animal, and plant health 🦠

ASM@asm.org · 8mo ago

🎉 #JVirology is pleased to announce the selectees for our inaugural New Voices in Virology collection! Chosen from 275+ applicants, these early-career scientists stood out for their creative proposals & strong career trajectories. ➡️ Meet the New Voices: asm.social/2HY

Feeling festive? Why not deck the halls with @cvrinfo.bsky.social's papercraft #VirusSnowflakes and celebrate the science of viruses and the fight against viral diseases. Download for free: cvr-engagement.co.uk/virus-snowfl... #scicomm #sciart #decorations

H3N2 preprint: there are concerns of a severe incoming influenza season due to the drifted H3N2 K clade. We at @psioxford.bsky.social analysed epi data and ran scenario models to see what we could discern about K clade transmission dynamics: zenodo.org/records/1770.... (1/18)

Excited to be part of this amazing group of virologists! @asm.org journals.asm.org/journal/jvi/...

New Voices in Virology

Annual competition for early-career virologists to publish a minireview in JVI. Their minireviews will be peer reviewed & published in a collection.

journals.asm.org

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. 🇫🇷

I gave a talk last year at TEDxNewEngland aimed at introducing the idea of viral sociality to a general audience, including implications for evolution & virology. Video now available online below. #socialviruses #evosky #virosky 🧪

The social lives of viruses | Asher Leeks | TEDxNewEngland

YouTube video by TEDx Talks

youtube.com

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 🇯🇵✨

🚨 DPhil opportunity at Pandemic Sciences Institute🚨 Excited to be co-supervising a new DPhil theme with Christophe Fraser and Yvonne Jones on Developing methods for accurate reconstruction of viral histories to guide pandemic preparedness & targeted interventions. Read more here: lnkd.in/eJXSXkia

We are thrilled to welcome the members of our new Early Career Researcher Advisory Panel! Discover more about the researchers who are helping shape the future of scientific communication: buff.ly/5abtNWQ #ECR 🧪

“Fast change, little spread” The University of Oxford’s Prof Katrina Lythgoe and Dr. Mahan Ghafari unpack ONS-CIS data on 576 persistent infections, rapid within-host evolution, and rare transmission after 1 month. #IDsky #MEDsky Read our Q&A: www.contagionlive.com/view/persist...

Persistent SARS-CoV-2 Infections in the Community Show Fast Within-Host Change but Little Late Transmission

Oxford’s Prof Katrina Lythgoe and Mahan Ghafari, DPhil, report ONS-CIS data on 576 persistent UK infections with rapid within-host evolution and rare transmission after one month.

contagionlive.com

🚨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!

Spyros Lytras@spyroslytras.bsky.social · last yr.

Some very inspiring science at #ismb2025 in Liverpool this week! And great to see lots of Glasgow friends! 😁 Unfortunately had to dip early to get to Oxford! Giving a talk on structural phylo and discussing some exciting projects with @mghafari.bsky.social tomorrow!👀👀

Very grateful to the @biology.ox.ac.uk for the kind spotlight — and for the opportunity to do meaningful work alongside such brilliant and thoughtful colleagues across Biology, Pandemic Sciences Institute, and Lincoln College. #GlobalHealth #VirusEvolution #PandemicPreparedness

Oxford Biology@biology.ox.ac.uk · last yr.

Outbreaks and inequities 🦠 @mghafari.bsky.social is tracing viruses back through time — not just to illuminate potential threats, but also to build more equitable and effective responses to epidemics and pandemics. Read our new spotlight on Mahan! 👇 bit.ly/4m8sSDO

I don’t have the words to describe what it feels like to watch my home city of Tehran and the neighbourhoods I haven’t seen in almost a decade, now burning on the news. Then getting messages from family and friends asking where it’s safest to flee, with empty pockets and no fuel to escape.

When I abruptly left my PhD in the US in 2017 and moved to the UK — ‘mastered out,’ as they say — many told me I shouldn’t have. That it was all just temporary. That it would pass soon enough…

BNO News@bnonews.com · last yr.

BREAKING: Trump signs travel ban for citizens from 12 countries, including Iran, Haiti, Somalia, and Sudan - CBS