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...

Very nice reporting on the importance—and the vulnerability— of model organism databases www.nature.com/articles/d41...

New exciting resource published!! The Viro3D paper is out, describing our comprehensive database of predicted virus protein structures! 💻🧬 Work with @ulad-litvin.bsky.social , @grovearmada.bsky.social , Alex Jack, @bljog.bsky.social , @davidlrobertson.bsky.social www.embopress.org/doi/full/10....

🚨 New Web Resource Alert! 🚨 We're delighted to share Viro3D a database of >85000 viral protein structure predictions from >4400 human & animal viruses. 🔗 viro3d.cvr.gla.ac.uk 📄 www.embopress.org/doi/full/10.... @molsystbiol.org @cvrinfo.bsky.social @uofgmvls.bsky.social #Virology #AlphaFold 🧪 🦠

🌊 Coronaviruses likely acquired their spike proteins from aquatic herpesviruses. 4/5

🔍 Searches against structural network are extremely sensitive and allow to recover more RdRps than iterative profile-based searches. 3/5

🦠 The diversity of viral proteins can be reduced to 19,000 structural clusters. A structure-similarity network captures relationships between them. 2/5

Viro3D paper is out! We predicted 85,000 protein structures from human & animal viruses. 1/5 🧵 📑 Paper doi.org/10.1038/s443... 🔭 Explore virosphere viro3d.cvr.gla.ac.uk

Great to have this one published @cp-cellreports.bsky.social !! Some sarbecoviruses can use more ACE2 orthologs than others. The reason? A few sites in the RBD modulating the receptor usage of these viruses throughout their evolution! Worth a read 👇👇👇 www.cell.com/cell-reports...

@zachhensel.bsky.social and I have a new paper on the origin of SARS-CoV-2! 🧪 There are a lot of reviews on the topic already, so we tried to do something different: characterize "lab leak" scenarios, and directly address those on SARS-CoV-2's furin cleavage site.▫️1/9 doi.org/10.5802/crbi...

Mosquito-borne viruses surge in a warming Europe | Science | AAAS www.science.org/content/arti...

Really excited to have been a small part of this work investigating sarbecovirus host range, receptor usage and antigenicity! www.biorxiv.org/content/10.1101/2025.09.03.673949v1

A common type of ant in Europe breaks a fundamental rule in biology: its queens can produce male offspring that are a whole different species go.nature.com/4mOb5T9

Experimental infections reveal unexceptional viral tolerance in bats https://www.biorxiv.org/content/10.1101/2025.08.28.672855v1

🚨1000 authoritarian actions. 7 months🚨 I've been tracking Trump's authoritarian actions. From dismantling democratic institutions to militarising immigration enforcement, Trump is reshaping America. In my new post I highlight key authoriarian attacks christinapagel.substack.com/p/grand-desi... 1/2

📢 VACANCY | Research Assistant/Associate - Data Analysis Support @drtoniho.bsky.social & @louisapollock.bsky.social's Pfizer-funded research project focused on effectiveness of maternal #RSV vaccination in infants in Scotland. More: bit.ly/CVR-WorkWithUs Apply: gla.ac.uk/explore/jobs/ Ref 180274

Excited to share our work at the interface of virology and AI at two upcoming events! Will present Viro3D (our virus structure database: viro3d.cvr.gla.ac.uk), recent Nature paper on Flaviviruses (www.nature.com/articles/s41...), plus brand new work. #Virology #AI #Research

That's right. Gift link www.nytimes.com/2025/08/18/o...

Biologists, virologists, evolutionary biologist, and public health experts have much to learn from climate scientists on tackling misinformation. This is the model to follow and the culture to foster:

📢 Calling all Postgrad Virologists! 🦠 Postgraduate Virologists Network are hosting their first conference for virology students, by virology students. 📍 @uofglasgow.bsky.social 📆 8-9 September Register and submit an abstract: www.postgradvirologistsnetwork.co.uk/2025-meeting

Come work with us👇

Research from USDA points to viruses spread by pesticide-resistant mites, indicating a worrying trend. Learn more on #NationalHoneyBeeDay: https://scim.ag/45zlFpJ

Check out our latest preprint led by Jumpei Ito and @shusukekawakubo.bsky.social !! PLANT 🌱 a protein language model for predicting antigenic cartography! PLANT takes HAs and predicts antigenic map coordinates, allowing for a deep dive into flu antigenic evolution! www.biorxiv.org/content/10.1...

This week @science.org examines the wonders of the immune system! From molecular defences that co-evolved with pathogens to specialised cells that are intricately linked with physiology, the immune system is attuned to biological sex and different stages of life.

📰 DEFRA avian influenza update on 06 Aug 2025 #IDEpi #OneHealth 🧪 🐔 HPAI H5N1 confirmed in commercial poultry at premises near Attleborough, Norfolk. 📊 74 confirmed HPAI H5N1 cases in poultry & other captive birds in UK from 04 Nov 2024. 🏴󠁧󠁢󠁥󠁮󠁧󠁿 England: 65 🏴󠁧󠁢󠁳󠁣󠁴󠁿 Scotland: 3 🏴󠁧󠁢󠁷󠁬󠁳󠁿 Wales: 2 🇬🇧 Northern Ireland: 4

In the arms race between viruses and their hosts, viruses have found a dependable ally..

RFK and other leaders have gotten popular by spreading false rumors about mRNA vaccines. It's not surprising to see them follow through, now cancelling $500m in mRNA vax contracts. Misinformation has real-life consequences. ICYMI my last piece: kffhealthnews.org/news/article...

"Its political leadership has shredded the NIH playbook so thoroughly [.] that even at current funding levels they are unable to perform their core work of.." It's not just budgets. Severe damage has already been done and continues to be done. www.theatlantic.com/health/archi...