Gytis Dudas

Great story! (Although I think that this is a TE, not an endogenous retrovirus)

Invasive mosquito vector species detected in surveillance traps in United Kingdom

LRP8 is a receptor for tick-borne encephalitis virus - Nature LRP8, an apolipoprotein E and reelin receptor with high expression in the brain, is a receptor for tick-borne encephalitis virus.

LRP8 is a receptor for tick-borne encephalitis virus

www.nature.com/articles/s41...

Quantifying viral load and characterizing virus diversity in wildlife samples with target enrichment sequencing Metagenomics is a powerful tool for characterizing viruses, with broad applications across diverse disciplines, from understanding the ecology and evolutionary history of viruses to identifying causat...

Excited to share that our paper on the relationship between viral load and metagenomic outputs in wildlife samples is now published in Microbial Genomics @microbiologysociety! 🎉 Fantastic collaboration with a brilliant team.

More info: 📖 tinyurl.com/ywb7tvjm

Viro3D: a comprehensive database of virus protein structure predictions | Molecular Systems Biology imageimageViro3D provides proteome-level, high confidence AI-protein structure predictions for >4,400 viruses, allowing mapping of form and function across the human and animal virosphere. Viro3D i...

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....

EMBO Young Scientists Forum 2025 in Vilnius wrapped up today. Huge thanks to fellow organisers, volunteer teams, @itaiyanai.bsky.social for a wonderful Night Science workshop & all speakers & attendees. Here's fellow organiser Stephen Jones taking YSF attendee entertainment to the next level.

> be at conference
> slide mentions human roseolovirus 6 beta
> don't know what that is
> ah, *technically* it's Roseolovirus humanbeta6b (in italics too)
> googling says it's actually just good old human herpesvirus 6

Thanks, ICTV 👍👍👍 I see your "facilitating communication" is going real well.

That's >10 yrs of undetected flu D circulation in cattle, an animal humans interact with & depend on. That reflects very poorly on our surveillance efforts & there's many other examples of late virus discovery - Tilapia lake virus, human metapneumovirus, etc. We need to do better. 6/6

Influenza A-D viruses are more closely related to flu in fish than to each other. To me that implies a propensity to spillovers into mammals directly from fish/amphibians or via unknown hosts. Assuming current flu D diversity dates back to its spillover means it happened in 1998. 5/6

Having said that, I see an interesting metagenomic angle here. @eddieholmes.bsky.social, @marypetrone.bsky.social & many others have revolutionised our understanding of influenza virus evolution over the last decade, showing a smooth continuum of influenza virus diversity in fish & amphibians. 4/6

Importantly, our results also seem to be heavily influenced by available sequence data. Even though we reconstruct the origin of current flu D HEF gene diversity as US or Japan, we aren't fully convinced by this. With limited location sampling at this time, substantially more data are needed. 3/6

Indrė, as a data sciences MSc, has done an excellent job at collating sequence & predictor data for a BEAST GLM, even teaching me a few things along the way. Our results implicate (weakly) cattle trade & short distance (shared land border and intra-continental) migrations in moving flu D around. 2/6

My MSc student Indrė Blagnytė has a #preprint up on @biorxivpreprint.bsky.social on influenza D virus: www.biorxiv.org/content/10.1.... Flu D was discovered back in 2011, mostly circulating in cattle. Despite lots of research, a comprehensive analysis of its phylogeography had been missing. 1/6

Heterogeneity in inhibition of genetically diverse dengue virus strains by Wolbachia The release of Aedes aegypti mosquitoes transinfected with the virus-inhibiting Wolbachia bacterium has the potential to reduce the burden caused by dengue virus (DENV). However, the robustness of thi...

📢New preprint on the impact of dengue virus genetic diversity on inhibition by Wolbachia 🦟🦠🧬

Project led by Afeez Sodeinde, @emiliefinch.bsky.social, and @keli5734.bsky.social! ✨

Key findings in thread below 👇

www.biorxiv.org/content/10.1...

An AI for an AI: identifying zoonotic potential of avian influenza viruses via genomic machine learning Avian influenza remains a serious risk to human health via zoonotic transmission, as well as a feasible pandemic threat. Although limited zoonotic cases have resulted from the current epizootic outbre...

🚨📝 New work via @thepandemicinst.bsky.social now preprinted!

We took ~19000 sequences of avian influenza virus and trained machine learning models on >40000 genomic/proteomic features - the resulting ensemble can predict zoonotic potential with AUC=0.95. More below!

www.biorxiv.org/content/10.1...

@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...

We just went through the submission process with a Lancet sub-journal for consideration of our latest preprint.

Then we got to the "fees" page - more than $8,000.

I'm not sure journals realize how squeezed ID funding is, but what I'm not going to spend eight grand of tax-payer money on is that.

Agree & I think @embo.org made the right move - preprints with outsourced peer-review (e.g. Review Commons) count as full publications for grant apps. I'd like to think that a peer endorsement system of preprints might work, can't be worse than predatory journals publishing any crap for money.

Understanding the future risk of bat coronavirus spillover into humans: correlating sarbecovirus receptor usage, host range, and antigenicity. Sarbecoviruses interact with their receptor, angiotensin converting enzyme 2 (ACE2), via the receptor binding domain (RBD) of Spike, the immunodominant target for neutralising antibodies. Understandin...

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

Near real-time data on the human neutralizing antibody landscape to influenza virus to inform vaccine-strain selection in September 2025 The hemagglutinin of human influenza virus evolves rapidly to erode neutralizing antibody immunity. Twice per year, new vaccine strains are selected with the goal of providing maximum protection again...

In new study led by @ckikawa.bsky.social, we provide near real-time data on human neutralizing antibody landscape to influenza by measuring ~26,000 titers to >100 recent viral strains

Data can inform vaccine selection & evolutionary/epidemiological modeling
www.biorxiv.org/content/10.1...

The 16th Ebola Virus Disease Outbreak in Bulape Health Zone, Kasai, Democratic Republic of the Congo: A new spillover event from an unknown reservoir host Background The Democratic Republic of the Congo (DRC) is currently facing concurrent outbreaks including mpox, cholera and malaria (1-4). The Ministry of Public Health, DRC has declared the 16th Ebola...

In under 24h following the newly identified outbreak of #Ebola in the DRC, the virus has been isolated, sequenced and the virus sequence data made publicly available.
virological.org/t/the-16th-e...

Last week we had a 3-day lab retreat at Vilnius University's base in Puvočiai with Lander de Coninck & @ingrida.bsky.social joining us as visitors. These retreats keep getting better & more productive thanks to the students & especially fellow PI @mgabrielaite.bsky.social. I'm super proud!

A short blog post about a recent preprint (work hatched as a very fun all-postdoc collaboration at @sfiscience.bsky.social)

"Last week’s attack on the #CDC could have been a slaughter."

Absolutely.

And, importantly, thanks to the inflammatory rhetoric, falsehoods, disinformation, and conspiracy theories constantly spouted by the very same person who's responsible for the agency - HHS Secretary RFK Jr.

He must go.

Just a reminder that if you want to do your postdoc in the best city in the world, well, you might be in luck - our position is still open and we're hoping to fill it within the next couple of weeks, so hurry up!

🤦‍♂️

Hypermutable hotspot enables the rapid evolution of self/non-self recognition genes in Dictyostelium Cells require highly polymorphic receptors to perform accurate self/non-self recognition. In the amoeba Dicytostelium discoideum, polymorphic TgrB1 & TgrC1 proteins are used to bind sister cells and e...

I'm excited to announce our new biorxiv preprint, wherein we investigate the evolution of the weirdest genetic locus I've ever seen! Behold the tgr genes of the social amoeba, which mediate self/non-self discrimination during facultative multicellularity 🐅 🧵 1/
www.biorxiv.org/content/10.1...

"On the one hand, we have a hypothesis underpinned by evidence, although imperfect, and on the other hand we have a hypothesis without evidence, although it might exist."

Our latest editorial in advance of our August issue

www.thelancet.com/journals/lan...

#IDSky #ClinMicro #ViroSky #SARS-CoV-2

Real-time, multi-pathogen wastewater genomic surveillance with Freyja 2 Case-based infectious disease surveillance is fundamental to public health, but is resource-intensive, logistically complex, and prone to sampling bias. Wastewater testing and sequencing have increasi...

A few days ago we preprinted our Freyja 2 paper, describing the expansion of our original Freyja method to a real-time, multi-pathogen surveillance tool to track pathogen lineage prevalence and dynamics from sequencing of wastewater and other complex samples (like milk). 🧵
 doi.org/10.1101/2025...

Our lab is helping with the organisation of this year's EMBO YSF. We have a great line up of invited speakers from (mostly) the wider Baltic region & a @nightsciencepod.bsky.social workshop on creativity in science (I did it a couple of years ago, it was awesome). Please share & consider joining us!