Sofia Paraskevopoulou

TSniffer: unbiased de novo identification of RNA editing sites and quantification of editing activity in RNA-seq data link.springer.com/article/10....

A public health perspective of SARS-CoV-2 evolution and surveillance strategies in Germany from 2020 to 2023 - Communications Medicine Oh, Hölzer et al., discuss the multidisciplinary approach used for monitoring the genomic and virological evolution of SARS-CoV-2 during the COVID-19 pandemic and its implications on public health in ...

🦠 Wie hat sich #SARS-CoV-2 in 🇩🇪 von 2020-2023 entwickelt?

In einem großen Review von RKI-Forschenden werden virologische Grundlagen, Variantenentwicklung, klinische Aspekte und die Rolle der Genomüberwachung beleuchtet.

Fazit: Auf die Interdisziplinarität kommt es an! 🤝

➡️ doi.org/10.1038/s438...

Taxonomic expansion and reorganization of Flaviviridae - Nature Microbiology Analysis of RNA polymerase hallmark gene phylogenies supported by protein structure relationships of flaviviruses and ‘flavi-like’ viruses underpins the taxonomic expansion and reorganization of Flaviviridae.

A #taxonomic revision of the human/animal RNA viruses #Flaviviridae identifies 4 divergent RdRP clades and restructures 12 genera across 3 families within Amarillovirales. #VirusEvolution
📄 https://doi.org/10.1038/s41564-025-02134-0
👤 EVBC: P. Simmonds, A. Butković, J. Mifsud, M. Beer, J.H. Kuhn

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

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!

Monumental effort led by Peter Simmonds and Jens Kuhn to reorganize the Family Flaviviridae based on analysis of RNA-directed RNA polymerase (RdRP) hallmark gene sequences is finally out. Enjoy reading. #ICTV @utmbhealth.bsky.social @astmh.bsky.social @sbvirologia.bsky.social

New publication alert!
Fertilization impacts microbiomes along the grassland trophic chain academic.oup.com/ismecommun/a...

#organicfertilizers #landusechange #microbiome #grasslands #onehealth

Book cover of “What Is Life? Revisted” by Daniel J. Nicholson, in the Cambridge Elements: The Philosophy of Biology series. Against a black background, the title is surrounded by Ernst Haeckel’s illustrations of marine organisms—radial, symmetrical forms in vivid blues, oranges, reds, and greens.

New Element in the Philosophy of Biology series—free to download until Oct. 24! @djnicholson.bsky.social uncovers Schrödinger’s motivations for writing "What Is Life?", revisits its central arguments & examines the book’s lasting impact on cell & molecular biology👇 www.cambridge.org/core/element...

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.

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...

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

Endogenous viral elements in termite genomes reveal extensive diversity of deltaviruses and provide insights into their origins Deltaviruses are subviral agents of animals, which, in humans, require a hepadnavirus helper for transmission. The absence of deltavirus-like endogeno…

New paper alert 🎉
We explore the origins of deltaviruses and find they have infected and co-evolved with termites for 141 million years 🐜🕑🦴

This was a fascinating story to work on with @ariskatzourakis.bsky.social, Jose Gabriel and @anselmojiro.bsky.social

www.sciencedirect.com/science/arti...

Conference title: Dialectical Biology Today: Legacies of Richard Lewontin, and image of Lewontin in Black and White with intense expression in front of a chalkboard holding up a fist, When and Where Friday, October 10, 2025 11:30 am to Sunday, October 12, 2025 2:00 pm Music Room (218) Goldring Student Centre 150 Charles St W, Toronto, ON M5S 1K5 | and online via Zoom

I'm excited to share with you all a conference I'm planning Oct. 10-12: Dialectical Biology Today: Legacies of Richard Lewontin.

It will be hybrid in Toronto and on zoom, so please join us however you can! Register for zoom link here: ihpst.utoronto.ca/events/diale...

Endogenous viral elements in termite genomes reveal extensive diversity of deltaviruses and provide insights into their origins Deltaviruses are subviral agents of animals, which, in humans, require a hepadnavirus helper for transmission. The absence of deltavirus-like endogeno…

Endogenous Deltaviruses (EVEs) in termite genomes !

Augmentation of wastewater-based epidemiology with machine learning to support global health surveillance - Nature Water Wastewater-based epidemiology has already proven to be a powerful tool to monitor the spread of a number of diseases. This Perspective discusses the integration with machine learning, highlighting its...

🚨 New Perspective in Nature Water 🚰💻

"Augmenting wastewater epidemiology with machine learning" 🧠🌍

A huge interdisciplinary collab w/ amazing colleagues @rki.de & beyond! 🙌

Special thx to lead author PhD student Eva & shared last Christopher for this effort!

🔗 www.nature.com/articles/s44...

GitHub - jonas-fuchs/varVAMP: Design degenerated primers on highly variable alignments for full genome sequencing or qPCR. Specifically developed for viruses. Design degenerated primers on highly variable alignments for full genome sequencing or qPCR. Specifically developed for viruses. - jonas-fuchs/varVAMP

🚀 Excited to share our NatComm paper on varVAMP – a open-source tool for degenerate primer design in viral genome seq & qPCR!

🔬 Supports diverse viruses SC2, HEV, Polio ...
🤝 Built in collaboration with amazing virus experts

🔗 github.com/jonas-fuchs/varVAMP
🧬 nature.com/articles/s41467-025-60175-9

Molecular epidemiology and evolution of norovirus in Australia and New Zealand, 2018 to 2020 Norovirus causes an estimated 699 million cases of gastroenteritis and 219,000 deaths each year. Historically, novel strains with a genogroup II genotype 4 (GII.4) capsid have emerged every 3–5 yea...

What can wastewater tell us about viruses? 💩🚽🧬📈

During the COVID-19 pandemic many labs turned to wastewater monitoring to detect viruses. However, Prof White's group @unswbabs.bsky.social has been using wastewater for over 10 years to monitor circulating norovirus 🤮. 🧵

doi.org/10.1080/2374...

zeitung.faz.net/faz/geistesw...

This approach enabled us to infer a mechanistic model of behaviour change for the 2022 Mpox outbreak in Berlin. You can preprint here: www.researchsquare.com/article/rs-6... 5/5

Efficient and accurate simulation of infectious diseases on adaptive networks Author summary Infectious disease spreading is often affected by the dynamics of human-human contacts. These contact dynamics may change over time, and in direct response to infection kinetics, throug...

Very pleased to see our latest work on sampling of spreading processes on adaptive temporal network published at @plos.org Complex Systems!
Read more at doi.org/10.1371/jour... or find some information below
1/5🧵

Go, Elon, and Never Darken Our Doors Again The worst ultra-billionaire on Earth says he’s leaving government. Let’s hope he actually does it.

"Roughly 1,500 babies have been born HIV-positive every day since January 21, because Musk cut off their mothers’ medication." prospect.org/power/2025-0...

SARS-CoV-2 evolution on a dynamic immune landscape - Nature A modelling approach predicts SARS-CoV-2 variant dynamics on the basis of immunity and cross-neutralization, which was shaped by a region’s SARS-CoV-2 infection history.

Nature research paper: SARS-CoV-2 evolution on a dynamic immune landscape

https://go.nature.com/4aCPDem

You might be wondering why we haven't updated outbreak.info for months.

Well, the reason is that GISAID cut our access in January - as they did others. Without telling us.

After a ♾️ back and forth, that is now permanent.

More on that soon - and why GISAID should not be trusted with critical data.

New methods are revolutionizing biology: an interview with Martin Steinegger Martin Steinegger, who is the only non-DeepMind-affiliated author of the AlphaFold2 Nature paper, offers unique insights and personal reflections.

Happy to share this interview with Weijie Zhao from NSR at #OxfordUniversityPress. It covers questions I’m often asked—why I chose Korea, AlphaFold2, my unconventional journey into academia, and research insights. Thanks again for the fun conversation.
📄 academic.oup.com/nsr/article/...

EVE Meeting Expression of Interest

I'm thinking of organising a meeting on endogenous viral elements (RNA, DNA and retroviral) - if you'd potentially be interested, please fill out the form here - forms.gle/wrCiWMw4yXZe... - so I can gauge interest. Please RT or share with anyone maybe interested! 🧪🧬🖥️🦠 #virology #bioinformatics

Very glad to have participated in #ViBioM2025 and an honor to be in this panel! An amazing week of talks, posters, and discussing with colleagues at IHMT NOVA in Lisbon. Huge thanks to the @evbc.bsky.social and everyone in the organizing committee ✨😊
#VirusBioinformatics #IHMT #EVBC

What a week in Lisbon! 🇵🇹 ViBioM 2025 brought 150+ virus bioinformaticians from 34 countries to explore viral evolution, ML tools, & taxonomy challenges. 🌱 All plant-based thanks to @desafiovegetariano! Huge thanks to organizers, speakers, and community! #ViBioM2025 #Viromics

We just succeeded in formally linking a specific rodent species - the otherwise charming fire-footed rope squirrel - to the onset of a mpox outbreak in a primate species - sooty mangabeys. Here Kai’s report on the preprint we released yesterday 1/2

The Department of Health and Human Services (HHS) is being decimated right now. Mass layoffs happening across agencies (NIH, FDA, CDC etc).

Some employees found out by security badge being denied. Others got email.

Line outside Health Resources and Services Administration this AM shared with me:

RFK, Jr. Laying Off Entire Office Of Infectious Disease And HIV/AIDS Policy Robert F. Kennedy, Jr., the Secretary of Health and Human Services is reportedly laying off the entire Office Of Infectious Disease And HIV/AIDS Policy. Here's the impact

RFK, Jr. Laying Off the entire OIDP - Office Of Infectious Disease And HIV/AIDS Policy

Problem is: general public not aware of what OIDP stands for, let alone what it does - and why this vision, strategy and organization is crucial

Here's just a small segment of what OIDP:
🧵

Very happy to share this work on #SARS-CoV-2 dynamics!✨
Model based on immunity & cross-neutralization, considering the variants' infection history of the population. @martinhoelzer.bsky.social and other colleagues at #RKI and #FUBerlin, congrats to all!