CLASV: Rapid Lassa virus lineage assignment with random forest Author summary Lassa fever is a viral illness that causes yearly outbreaks in West Africa and has the potential to spread internationally, with cases recently reported in several countries outside the region. Quickly identifying the genetic lineage of the virus responsible is critical for inferring the source of outbreaks and guiding medical and public health responses. However, tools designed specifically for rapid Lassa virus lineage identification are almost non-existent. In this study, we introduce CLASV, a fast and user-friendly tool that uses machine learning to identify the major circulating lineages of Lassa virus from genetic sequences. Validated on real-world data, CLASV achieved high accuracy even when working with incomplete sequences. It runs in minutes on a standard computer, making it practical for deployment in local low-resource laboratories. By providing timely and reliable lineage information, CLASV has the potential to enhance outbreak response and enable more targeted public health interventions—both in West Africa and in countries managing imported cases.

Introducing CLASV: a fast, Random-Forest-based tool for assigning #LassaVirus lineages (II, III, IV/V, VII) from raw sequences, deployable in low-resource settings and crucial for outbreak response. 🦠💻 #VirusBioinformatics
📄 https://doi.org/10.1371/journal.pntd.0013512
👤 EVBC: Denise Kühnert

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 delivers >85,000 AI-predicted protein structures for >4,400 viruses, expanding viral structural coverage 30-fold, enabling new insights to virus function/evolution.
#VirusBioinformatics #StructuralBiology🧬🔍
📄 doi.org/10.1038/s443...
👤EVBC members: Spyros Lytras, David Robertson, Joseph Hughes

Multidimensional analysis of host–virus interactions using the virus-encoded CRISPR-based direct readout system (VECOS) - Nature Protocols In the virus-encoded CRISPR-based direct readout system, single-guide RNA libraries are expressed directly from the genomes of viruses so that single-guide RNA abundance at distinct stages of the vira...

VECOS enables direct CRISPR-based investigation of host–virus interactions by embedding sgRNA libraries in viral genomes, yielding precise, multidimensional data on viral propagation dynamics.
#VirusBioinformatics #HostVirusInteractions 🔬🧬
📄 doi.org/10.1038/s415...
👤 EVBC member: Noam Stern-Ginossar

Targeted decontamination of #SequencingData with the #CLEANtool enhances viral #genome analysis accuracy #VirusBioinformatics #BioinformaticsTools #DataQualityControl 🧬🔬
📄https://doi.org/10.1093/nargab/lqaf105
👤EVBC: Marie Lataretu, Sebastian Krautwurst, Mike Marquet, Adrian Viehweger, Martin Hölzer

Investigating alveolar macrophages in an human ex vivo precision‐cut lung slice model of SARS‐CoV‐2 infection using Raman spectroscopy—A case study Label-free Raman spectroscopy is utilized for an in-depth characterization of alveolar macrophages directly within intact precision-cut human lung slices. Characteristic biochemical changes in indivi...

#RamanSpectroscopy enables label-free, 3D phenotyping of alveolar macrophages during SARS-CoV-2 infection in ex vivo human lung tissue - achieving 83% accuracy in distinguishing infected cells via LDA analysis
#VirusBioinformatics
📄 https://doi.org/10.1002/ctm2.70453
👤 EVBC: Stefanie Deinhardt-Emmer

A More Rapid Method for Culturing LUHMES-Derived Neurons Provides Greater Cell Numbers and Facilitates Studies of Multiple Viruses The ability to study mature neuronal cells ex vivo is complicated by their non-dividing nature and difficulty in obtaining large numbers of primary cells from organisms. Thus, numerous transformed progenitor models have been developed that can be routinely cultured, then scaled, and differentiated to mature neurons. In this paper, we present a new method for differentiating one such model, the Lund human mesencephalic (LUHMES) dopaminergic neurons. This method is two days faster than some established protocols, results in nearly five times greater numbers of mature neurons, and involves fewer handling steps that could introduce technical variability. Moreover, it overcomes the problem of cell aggregate formation that commonly impedes high-resolution imaging, cell dissociation, and downstream analysis. While recently established for herpes simplex virus type 1, we demonstrate that LUHMES neurons can facilitate studies of other herpesviruses, as well as RNA viruses associated with childhood encephalitis and hemorrhagic fever. This protocol provides an improvement in the generation of large-scale neuronal cultures, which may be readily applicable to other neuronal 2D cell culture models and provides a system for studying neurotrophic viruses. We named this method the Streamlined Protocol for Enhanced Expansion and Differentiation Yield, or SPEEDY, method.

The SPEEDY method boosts LUHMES derived neuron yield for scalable studies of neurotropic viruses – faster and more reproducible for HSV 1, Zika, measles, and filovirus systems.
#mpox #NeuronModels #VirusBioinformatics #CellCultureAdvancement
👤EVBC: Lars Dölken
🔗

Redirecting

Genome-wide screening reveals TRIM48 as a novel negative regulator of RIG I antiviral signaling, informing host–virus interaction studies.
#VirusBioinformatics #InnateImmunity #TRIM48
👤EVBC: Lars Kaderali 
🔗

DIGGER 2.0: digging into the functional impact of differential splicing on human and mouse disorders Abstract. Changes in alternative splicing between groups or conditions contribute to protein–protein interaction rewiring, a consequence often neglected in

Discover a new tool: DIGGER 2.0 enables splice-aware functional annotation of interaction network changes using RNA seq analysis via NEASE.
#VirusBioinformatics #AlternativeSplicing #InteractomeTools

📄 doi.org/10.1093/nar/...
👤EVBC: Olga Kalinina

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

🧬 ECR Viromics Webinar Series
Join us on April 9, 2025, for an exciting talk by @Marcel Ribeiro-Dantas
"Nextflow Pipelines: Connecting Data to Discoveries"
📅 Time: 10 AM EST | 4 PM CET
🔗 Register evbc.uni-jena.de/events/ecr-v...
#Viromics #Nextflow #VirusBioinformatics #Seqera

🔬 RDRP Summit 2025 – A Satellite Event of ViBioM 2025!
Portugal! 🌍

📅 May 11–12, 2025
🔗 Register Now: rdrp.io
📢 We look forward to seeing you in Lisbon!

#RdRpSummit2025
#Bioinformatics
#VirusBioinformatics

🚀 ViBioM 2025 – Join Us in Lisbon!

📅 Dates: 13–15 May 2025
📜 Abstract Submission Deadline: 28 February 2025
🔗 Register Now: evbc.uni-jena.de/events/vibio...

🔬 Our Invited Speakers:
👉 evbc.uni-jena.de/events/vibio...

#ViBioM2025 #Virology #Bioinformatics #VirusBioinformatics

In our December #virusesinsilico lecture, Naeim Moafinejad will present SimRNAweb v2.0, a web server for RNA folding simulations and 3D structure modeling.
#RNAfolding #RNAviruses
Registration is free: evbc.uni-jena.de/events/virus...
#VirusBioinformatics

Addressing pandemic-wide systematic errors in the SARS-CoV-2 phylogeny The SARS-CoV-2 genome occupies a unique place in infection biology – it is the most highly sequenced genome on earth (making up over 20% of public sequencing datasets) with fine scale information on s...

#SARSCoV2 #Phylogenetics: A high-quality global tree of 4.4M samples built with the novel Viridian tool tackles #pandemic-wide systematic errors. #VirusBioinformatics

📄 doi.org/10.1101/2024...
EVBC👤: Martin Hölzer

Redirecting

Benchmarking sequencing technologies for #wastewater-based #SARSCoV2 #surveillance reveals trade-offs between cost, timeliness, and accuracy.
#VirusBioinformatics #WastewaterEpidemiology #SARSCoV2Surveillance #NGS

📄 doi.org/10.1016/j.wa...
EVBC👤: Niko Beerenwinkel

Population dynamics of defective viral genomes of tomato black ring virus during host-to-host transmission | Journal of Virology Defective viral genomes (DVGs) have been identified in vivo and in vitro for different virus species infecting humans, animals, and plants. The ability to form DVGs during the passaging of virus in on...

Investigating tomato black ring virus DVGs! This study uncovers the impact of host-to-host transmission on viral evolution, with deletions dominating in diverse host species.
#VirusBioinformatics #DVGs #PlantVirology

📄 doi.org/10.1128/jvi....
EVBC👤: @sfelena.bsky.social

PNAS Proceedings of the National Academy of Sciences (PNAS), a peer reviewed journal of the National Academy of Sciences (NAS) - an authoritative source of high-impact, original research that broadly spans...

Unraveling Hepatitis E virus in neurons: A novel human model shows HEV impacts neurite growth with limited immune response. A step closer to understanding HEV-associated neurological disorders! #VirusBioinformatics #HEV #Neurovirology

📄 doi.org/10.1073/pnas...
EVBC👤: @compvirol.bsky.social

A virus associated with the zoonotic pathogen Plasmodium knowlesi causing human malaria is a member of a diverse and unclassified viral taxon Abstract. The Apicomplexa are a phylum of single-celled eukaryotes that can infect humans and include the mosquito-borne parasite Plasmodium, the cause of

Discovering the unseen: A novel RNA virus in Plasmodium knowlesi reshapes our understanding of ormycovirus diversity and protozoan viromes! 🌍🔬

📄 doi.org/10.1093/ve/v...
EVBC👤: Justine Charon

#VirusBioinformatics #Metagenomics #ZoonoticViruses #Malaria

🚨 Save the Date! 🚨
We're excited to announce #ViBioM2025, the International Virus Bioinformatics Meeting, happening 13–15 May 2025 in Lisbon, Portugal! 🦠💻
Stay tuned for further details: evbc.uni-jena.de/vibiom2025/
#VirusBioinformatics

The EVBC extends warm wishes to you and your loved ones for a joyous holiday season. Here's to a new year filled with exciting breakthroughs, meaningful collaborations, and continued progress in our collective mission. #virusbioinformatics #MerryChristmas #HappyNewYear

What better way to end the year than announcing the exciting first batch of the keynote speaker line-up for #ViBioM2024? #keynotespeakers #virusbioinformatics

🎤 Nathan Grubaugh
🎤 Mart Krupovic
🎤 Houriiyah Tegally
🎤 Lia Van Der Hoek
🎤 Vera van Noort

EVBC Newsletter 78 / December 2023 includes a #virusbioinformatics tool, upcoming international events, keynote speakers + key dates for #ViBioM2024 and a vacancy at Wageningen University.
t.co/q7cS9PZSSU

Here we go again: Mark your calendars for the International #VirusBioinformatics Meeting 2024 and join us in Leuven, May 28-30, 2024! Organized together with KU Leuven
and Université libre de Bruxelles. Stay tuned for more updates and registration details. #SaveTheDate #ViBioM2024