Meet Tania Dottorini , Editor-in-Chief of Microbiology Horizons - a journal advancing open, reproducible, and interdisciplinary research, bringing together authors, reviewers, editors, academics and policymakers to tackle global challenges. https://microb.io/4ttwnbm

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/...

Listen to Kieran's recent presentation at the AVE Virology Interest Group "Characterizing novel viral proteins using protein language models (PLMs)": youtu.be/phrIC-J5Je0?...

New paper👇🦠

Maybe you heard somewhere that the COVID-19 pandemic started with a lab leak? NO! That is NOT what the evidence shows. It was not a goddamn lab leak. I’ve had enough. Here is what the evidence shows: it was zoonotic spillover at the market rasmussenretorts.substack.com/p/five-reaso...

H5N1 in dairy cows largely has disappeared from the news--a reflection of steeply declining detections. But it continues to circulate on dairies, and researchers continue to debate critical questions about how the virus moves between farms and within herds. www.science.org/content/arti...

🦅 What’s driving the spread of highly pathogenic avian influenza (H5N1) across Europe? Using machine learning and wild bird ecology, a new study from @L_Brierley & colleagues reveals a shift towards year-round risk in cold, low-lying regions of NW Europe. www.nature.com/articles/s41...

📢 Fellowship Sponsorship at the CVR 📆 Deadline: Tues 21 April 26 We have an open sponsorship process and are committed to supporting a diverse, inclusive & well-supported community. Full support with application writing, organising peer reviews and interview prep. gla.ac.uk/research/az/...

Read @flodebarre.bsky.social's original analysis: pandemonium.hypotheses.org/898. While the original WeChat post is bonkers, it points to unreleased data from the market, including: 1️⃣ Potentially infected animals in "Stall A" - the hot-spot inside the market. 2️⃣ +Serology of vendor from Stall A.

In 2021, amid debate over COVID-19’s origin, a viral WeChat post claimed the virus came to China from Maine on frozen lobsters sold at the Wuhan market. Scientists dismissed it—but a new analysis suggests the bizarre claim might hint at missing data China hasn’t released. https://scim.ag/47yG2F6

A ludicrous theory posted on WeChat by "Kunlun Sword" in 2021 asserted that Maine lobsters sparked the COVID pandemic. Evobiologist Flo Débarre now has found clues in the post that suggest China has withheld evidence about early infected humans and animals. www.science.org/content/arti...

The value of virological research in wildlife journals.asm.org/doi/10.1128/...

1/ 🦟 Big news: #Pathoplexus now supports Dengue virus & Yellow Fever virus - two arboviruses responsible for over 400 million infections and up to 94,000 deaths per year. Here's what’s new in our latest update 👇🏻 Read the full update: pathoplexus.org/news/2026-03... 📰

Transient RNA structures play a key role in the emergence of highly pathogenic avian influenza viruses! Great to see this collaboration with Mathis Funk, Mathilde Richard, Stephen Cusack, and others in @science.org www.science.org/doi/10.1126/...

Glad to see our recent paper getting some coverage @nytimes.com. Fun little study with some key findings for understanding zoonosis and viral emergence.

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

"Russian flu," the pandemic that hit in 1977, bears an evolutionary signature of having emerged from a lab, perhaps as part of a failed vaccine effort. Covid, mpox, Ebola, and other influenza pandemics don't. Here's my story on a new way to trace the origins of pandemics. Gift link: nyti.ms/46N0W33

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.

The AlphaFold Database, jointly developed with Google DeepMind, now contains datasets from specialist communities. This includes rich datasets for microbes, viruses & parasites associated with tropical diseases. Explore the new datasets in the AlphaFold Database. www.ebi.ac.uk/about/news/u...

Massive cuts to global health-care funding have had a huge impact on Africa, but a more resilient system can be built from within go.nature.com/46RnW0G

Staff at NIAID have been instructed to remove the words “biodefense” and “pandemic preparedness” from the US institute’s web pages, according to e-mails Nature has obtained. Read more about the shift in direction for NIAID. go.nature.com/4twztMV

After more than 1.2 Americans lost their lives to Covid, NIH director Jay Bhattacharya orders the agency to deprioritize pandemic preparedness & biodefense. Make it make sense. Scoop from @maxkozlov.bsky.social @nature.com www.nature.com/articles/d41...

A long time ago in a galaxy far away, there was a SARS-CoV-2 pandemic. Our paper, led by @martibartfast.bsky.social a) correcting errors in 4.5 million genomes & their phylogeny b) improving representation of the Global South in public data www.nature.com/articles/s41... (thread 1/n)

We’re excited to announce our 9th Introduction to Viral #Bioinformatics course, starting 15 June 2026! 🧬 @cvrinfo.bsky.social Course information👉 tinyurl.com/yc8285zd

The US withdrawal from #WHO became official today, leaving the world less prepared for dangerous disease outbreaks. “When that will bite us in the ass, it’s impossible to predict. But there is a 100% certainty that it will bite us in the ass,” one expert told me. www.statnews.com/2026/01/22/u...

We've a computational PhD project available AI-DRIVEN DISCOVERY OF VIRUS–HOST MOLECULAR INTERACTIONS www.gla.ac.uk/colleges/mvl... as part of the University of Glasgow's MVLS Futures Themes PhD Programme. Deadline for applications is this Monday, 12th Jan 2026. Please apply!

We've a computational PhD project available AI-DRIVEN DISCOVERY OF VIRUS–HOST MOLECULAR INTERACTIONS www.gla.ac.uk/colleges/mvl... as part of the University of Glasgow's MVLS Futures Themes PhD Programme. Deadline for applications is this Monday, 12th Jan 2026. Please apply!

Review of 200 novel human #viruses over a century a reminder that pathogen emergence isn’t rare Increased human-animal interaction, driven by factors such as urbanization and deforestation, has created new opportunities for pathogens to jump species. www.cidrap.umn.edu/m...

How does fever work? Our new Science paper shows how elevated body temperature can protect against severe influenza and that avian-origin viruses escape this defence. This is likely one reason why bird flus and some pandemic influenzas can be so severe.🧵 www.science.org/doi/10.1126/...

A study on 1.7 million people in Hong Kong shows superior hybrid immunity to Covid in people who got vaccinated before infection vs. people who got infected first. "Our findings are a direct rebuttal to arguments for natural immunity," the authors write. doi.org/10.1016/j.va...

Never a good sign when I have a chance to post this. www.usatoday.com/story/travel...

A nice article, highlighting the important work our collaborators in South Africa are doing using wastewater to surveil a bunch of different vaccine preventable diseases (and finding a lot more of them than other reports would make you believe…). 💪🇿🇦 www.nature.com/articles/d44...

NEW: We traced out a devastating outbreak of bird flu to its source: an egg farm in Ohio. Where the wind blew, the virus followed. Within weeks, the farms downwind were about 20 times as likely to see outbreaks as those that weren’t.

Human #BirdFlu case in WA. #H5N5 not #H5N1. Patient is severely ill. Update coming. www.latimes.com/science/stor...

New paper👇

To summarise, PLM-interact extends single-protein PLMs to jointly encode interacting partners. It achieves state-of-the-art performance in cross-species and virus–host PPI prediction tasks and can be fine-tuned to predict mutation effects in human PPIs.

PLM-interact was applied to virus–human PPI prediction. The model outperforms existing approaches, achieving 5.7%, 10.9%, and 11.9% gains in AUPR, F1, and MCC, respectively — effectively capturing virus–host interactions at the protein level.

We further demonstrate examples where PLM-interact correctly predicts the effects of mutations on PPIs associated with human diseases. These results highlight its potential to identify whether disease-associated mutations weaken or strengthen protein interactions.

We fine-tuned PLM-interact to predict the effects of mutations on protein interactions — identifying whether mutations increase or decrease interaction strength. The fine-tuned model significantly outperforms zero-shot PPI models in the mutation-effect prediction task.

PLM-interact achieves state-of-the-art performance on a widely adopted cross-species PPI prediction benchmark — trained on human data and tested on mouse, fly, worm, yeast, and E. coli.

Existing PPI models use pre-trained PLMs to embed each protein separately, ignoring amino acid interactions between proteins. PLM-interact goes beyond single-protein encoding by jointly representing protein pairs to learn their relationships.

Protein language models trained on massive protein sequence datasets capture evolutionary, sequence and structural features — becoming the method of choice for representing proteins in state-of-the-art PPI predictors.

This work is a part of my viroinf PhD research, carried out under the supervision of Craig Macdonald, @davidlrobertson.bsky.social, and Ke Yuan, with HPC support from DiRAC (www.dirac.ac.uk).

New paper👇

A divergent betacoronavirus with a functional furin cleavage site in South American bats https://www.biorxiv.org/content/10.1101/2025.10.24.684489v1

1. We ( @jbakcoleman.bsky.social, @cailinmeister.bsky.social, @jevinwest.bsky.social, and I) have a new preprint up on the arXiv. There we explore how social media companies and other online information technology firms are able to manipulate scientific research about the effects of their products.

There is one point of agreement among both enthusiasts and sceptics: the future has already arrived go.nature.com/3WL73iS

And now NextStrain as well. Next up, will GISAID start charging open-source community tools to have access? That would completely shaft users who contributed to GISAID, where we never agreed to that and assumed GISAID would be good custodians of the data we contributed. They're not.

We are at our future planning meeting with Genomics team at main campus of University 🏰 @cvrbioinfo.bsky.social

Chatbots are explicitly being designed “to elicit intimacy and emotional engagement in order to increase our trust in and dependency on them” (me in Wired magazine 🤭). This designed intimacy combined with AI sycophancy creates serious risks for delusional thinking www.wired.com/story/ai-psy...