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spyroslytras.bsky.social
Spyros Lytras
@spyroslytras.bsky.social
740 followers 640 following 120 posts
Evolutionary Virologist based at the University of Tokyo 🇯🇵 💻🦠🏳️‍🌈
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spyroslytras.bsky.social
Spyros Lytras @spyroslytras.bsky.social · May 10
Sooo happy to finally have this one published!! (3 years in the making… 👀) A comprehensive investigation into the recency and geographical origins of both SARS-CoVs that spilled to humans in the past few decades, now in @cp-cell.bsky.social www.cell.com/cell/fulltex...
The recency and geographical origins of the bat viruses ancestral to SARS-CoV and SARS-CoV-2
Recombination-aware evolutionary analyses of the entire genomes of SARS-CoV-1-like and SARS-CoV-2-like viruses indicate that SARS-CoV-1 and SARS-CoV-2 descend from bat coronaviruses that circulated as...
www.cell.com
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Reposted by Spyros Lytras
microbiologysociety.org
Microbiology Society @microbiologysociety.org · 1d
Huge congratulations to Emma Davis, the winner of 2025's Early Career Microbiologist of the Year prize! We agree with Emma that all of the finalists' talks were brilliant and a massive well done to everyone involved!
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spyroslytras.bsky.social
Spyros Lytras @spyroslytras.bsky.social · 22h
what a fantastic ted talk!! for those of you who haven't heard of "sociovirology" before or still wonder why it might be important this is the video to watch! 😁
asherleeks.bsky.social
Asher Leeks @asherleeks.bsky.social · 1d
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
www.youtube.com
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Reposted by Spyros Lytras
flodebarre.bsky.social
Flo Débarre @flodebarre.bsky.social · 4d
Interesting interview of @peterdaszak.bsky.social by @nicolascgrey.bsky.social on the personal consequences of having become a public villain in a set of conspiracy theories

www.thisrobotdreaming.com/blog/intervi...
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Reposted by Spyros Lytras
grovearmada.bsky.social
Joe Grove @grovearmada.bsky.social · 12d
🚨 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 🧪 🦠
Viro3D
viro3d.cvr.gla.ac.uk
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Reposted by Spyros Lytras
ulad-litvin.bsky.social
Ulad Litvin @ulad-litvin.bsky.social · 12d
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
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...
doi.org
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spyroslytras.bsky.social
Spyros Lytras @spyroslytras.bsky.social · 10d
The Viro3D database includes:

✅protein structures across the human and animal virosphere
✅comparative analysis between structures
✅interactive web interface
✅taxonomic indexing

We hope that this turns into a useful resource for all kinds of virologists!

Browse here: viro3d.cvr.gla.ac.uk
Viro3D
viro3d.cvr.gla.ac.uk
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spyroslytras.bsky.social
Spyros Lytras @spyroslytras.bsky.social · 10d
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....
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...
www.embopress.org
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Reposted by Spyros Lytras
recombconf.bsky.social
RECOMB Conference Series @recombconf.bsky.social · 12d
#RECOMB2026 will be in Thessaloniki, Greece on May 26-29, 2026. Satellites on May 24-25. Save the date!

Το συνέδριο #RECOMB2026 θα πραγματοποιηθεί στη Θεσσαλονίκη, στις 26-29 Μαΐου 2026. Οι δορυφορικές εκδηλώσεις θα διεξαχθούν στις 24-25 Μαΐου 2026. Σημειώστε την ημερομηνία!
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worobey.bsky.social @worobey.bsky.social · 18d
My understanding is that the situation for H1B visa holders outside the US today is urgent: if a current H-1B holder seeks entry into the U.S. after 12:01 a.m. EDT on September 21, 2025, it is too late to avoid the fee—entry will be restricted without the newly-imposed $100,000 employer payment.
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peterdaszak.bsky.social
Peter Daszak @peterdaszak.bsky.social · Aug 19
New paper from @naturehealthglobal.bsky.social scientists identifies extensive spillover risk of an under-researched group of coronaviruses in China and Southeast Asia. 🧵
naturehealthglobal.org/new-paper-id...
New Paper Identifies Widespread Risk Of Coronavirus Spillover In Pigs And People Across Southeast Asia And China - Nature.Health.Global
A new scientific paper from Nature Health Global scientists identifies widespread spillover risk of a group of coronaviruses in China and Southeast Asia.
naturehealthglobal.org
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spyroslytras.bsky.social
Spyros Lytras @spyroslytras.bsky.social · 18d
Arrived in gorgeous cote d' azur just in time for the first day on the European Meeting on Viral Zoonoses!

Aside from enjoying the weather and the wine I'll also be presenting some exciting (and still unpublished) work on novel sarbecovirus discovery! 🍷🏖️🦇
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spyroslytras.bsky.social
Spyros Lytras @spyroslytras.bsky.social · 18d
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...
Molecular basis of sarbecovirus evolution and receptor tropism in natural hosts, potential intermediate hosts, and humans
Kosugi et al. elucidate sarbecovirus evolution and ACE2 receptor tropism in natural hosts (12 Rhinolophus bat species), potential intermediate hosts (civets and raccoon dogs), and humans using a pseud...
www.cell.com
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saskiapopescu.bsky.social
Saskia Popescu @saskiapopescu.bsky.social · Sep 8
Dr. @angierasmussen.bsky.social breaking down current policies and the anti-vaccine trends/rhetoric within the US that will lead to significant global health ramifications - #19vaccinecongress
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angierasmussen.bsky.social
Angie Rasmussen @angierasmussen.bsky.social · Sep 7
At Vaccine, our editorial team is united to defend and support immunization and vaccine science around the world. I am so proud & honored to stand alongside these outstanding scientists & clinicians to prevent disease & save lives with integrity & courage.
A bunch of awesome looking vaccinologists standing on a balcony in Kyoto with a backdrop of forested hills
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spyroslytras.bsky.social
Spyros Lytras @spyroslytras.bsky.social · Sep 7
Great to be at Elsevier's 19th Vaccine Congress in beautiful Kyoto! 💉💉

An exceptionally important topic to global health, especially in the current political climate...
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carlzimmer.com
Carl Zimmer @carlzimmer.com · Aug 19
This summer's raging wildfires in Spain are the red spike in this graph. atmosphere.copernicus.eu/copernicus-i...
Graph showing wildfire carbon emissions in Spain. This year's fires are in a league of their own.
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Reposted by Spyros Lytras
angierasmussen.bsky.social
Angie Rasmussen @angierasmussen.bsky.social · Aug 12
The shooting at CDC was domestic terrorism. It was instigated by the HHS Secretary's years-long campaign against an agency he oversees.
open.substack.com/pub/rasmusse...
When Dissent Becomes Domestic Terrorism
The call is coming from inside HHS
open.substack.com
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spyroslytras.bsky.social
Spyros Lytras @spyroslytras.bsky.social · Aug 8
Fantastic work George et al!!!!
gbouras13.bsky.social
George Bouras @gbouras13.bsky.social · Aug 8
Stoked to finally have a preprint out for Phold, our tool that uses protein structural information to enhance phage genome annotation #phagesky 1/n

www.biorxiv.org/content/10.1...
Protein Structure Informed Bacteriophage Genome Annotation with Phold
Bacteriophage (phage) genome annotation is essential for understanding their functional potential and suitability for use as therapeutic agents. Here we introduce Phold, an annotation framework utilis...
www.biorxiv.org
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Reposted by Spyros Lytras
gbouras13.bsky.social
George Bouras @gbouras13.bsky.social · Aug 8
I also put together an extra ColabFold formatted database of nearly 130M phage proteins that can be used to make better viral protein structure predictions github.com/gbouras13/co...
GitHub - gbouras13/colabfoldv: Augmented Local MSA Generation for Phage and Viral Proteins using the ColabFold Framework
Augmented Local MSA Generation for Phage and Viral Proteins using the ColabFold Framework - gbouras13/colabfoldv
github.com
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Reposted by Spyros Lytras
gbouras13.bsky.social
George Bouras @gbouras13.bsky.social · Aug 8
c) With Phold we released more than 3M phage protein structure predictions (see the preprint for bulk download links), including a ColabFold generated proteome for each unique genus in INPHARED. We will make these more user-friendly soon.

For now see linsalrob.github.io/PHROG_struct...
PHROG Structure Gallery
linsalrob.github.io
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Reposted by Spyros Lytras
ariskatzourakis.bsky.social
Aris Katzourakis @ariskatzourakis.bsky.social · Aug 6
In the arms race between viruses and their hosts, viruses have found a dependable ally..
sheencr.bsky.social
Prof Sheena Cruickshank @sheencr.bsky.social · Aug 6
RFKJr’s gradual elimination of vaccines in USA is continuing and gathering pace as 22 federal contracts for mRNA-based vaccines being terminated including late stage research for bird flu vaccine #ImmunoSky 🧪🧵
RFK Jr’s health department to halt $500m in mRNA vaccine research
Agency to end 22 federal contracts, questioning safety of technology credited with helping end Covid pandemic
www.theguardian.com
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spyroslytras.bsky.social
Spyros Lytras @spyroslytras.bsky.social · Aug 7
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...
Integrative modeling of seasonal influenza evolution via AI-powered antigenic cartography
Seasonal influenza viruses evade host immunity through rapid antigenic evolution. Antigenicity is assessed by serological assays and typically visualized as antigenic maps, which represent antigenic d...
www.biorxiv.org
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angierasmussen.bsky.social
Angie Rasmussen @angierasmussen.bsky.social · Jul 25
They are really destroying all research on infectious diseases.
jeremymberg.bsky.social
Jeremy Berg @jeremymberg.bsky.social · Jul 24
And so it begins... NIAID has issued 20 R01s with 4 year budgets (i.e. Multi-year funded) since 7/7/25. These are almost unheard of in the past.
jeremymberg.bsky.social
Jeremy Berg @jeremymberg.bsky.social · Jul 23
In order to understand and communicate about the implications of this multi-year funding scheme, I put together a simple computer simulation.

1/n
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spyroslytras.bsky.social
Spyros Lytras @spyroslytras.bsky.social · Jul 24
If you're in Oxford tomorrow 👀👀
mghafari.bsky.social
Mahan Ghafari @mghafari.bsky.social · Jul 24
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!
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spyroslytras.bsky.social
Spyros Lytras @spyroslytras.bsky.social · Jul 24
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!👀👀
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