New study shows that avian origin #influenzaA #viruses with avian PB1 resist fever level temperatures in mammals, suggesting #fever can be a potent #antiviral defence but may fail against bird flu strains. 📄 https://doi.org/10.1126/science.adq4691  👤 EVBC members: Spyros Lytras, Edward Hutchinson

This new work develops light activatable RNase L ligands enabling spatiotemporal control of RNA degradation in cells as a host directed antiviral strategy. #Antivirals #RNA #Photopharmacology 📄 https://doi.org/10.1021/jacs.5c13457  👤 EVBC member: Volker Thiel

New Communications Biology article outlines parameter optimisation for #MINFLUX #microscopy to improve single particle tracking accuracy and extend measurable diffusion ranges in membranes. 🔬#Biophysics 📄 https://doi.org/10.1038/s42003-025-09060-1  👤 EVBC member: Christian Eggeling

New review highlights #SARS-CoV-2 evolution and longstanding #GenomicSurveillance in Germany, emphasising the need for adaptive #PublicHealth strategies for pandemic preparedness. 📄 https://doi.org/10.1038/s43856-025-01093-1  👤 EVBC members: Max von Kleist, Thorsten Wolff

The updated MODOMICS #database expands #RNAmodification annotations with transcriptome wide data, enhanced structural descriptors and interactive tools for the 20th anniversary. #Epitranscriptomics 📄 https://doi.org/10.1093/nar/gkaf1284  👤 EVBC members: Filip Stefaniak, Janusz Bujnicki

New preprint benchmarks #Nanopore direct RNA sequencing for quantitative m6A mapping, revealing best practice filters and cell type specific #epitranscriptomic differences in fibroblasts and neurons. #RNAseq 📄 https://doi.org/10.1101/2025.11.02.686099  👤 EVBC member: Daniel Depledge

New study shows older siblings and urban/rural residence strongly shape the infant gut virome at one year, with most exposure-linked vOTUs being phages. 🔬👶🌍 #Virome #InfantHealth 📄 https://doi.org/10.1080/19490976.2025.2501194 👤 EVBC members: Marie-Agnès Petit

HI-FEVER introduces a scalable Nextflow pipeline for rapid, high-throughput discovery and annotation of endogenous virus elements across host genomes. ⚡🧬 #VirusEvolution #Genomics #Bioinformatics 📄 doi.org/10.1093/bioi... 👤 EVBC members: Emma Harding, Cormac Kinsella

BV-BRC expands its unified platform for bacterial and virus genomics with new analysis tools, updated pipelines, and an AI Copilot for workflow guidance and data exploration. 🤖🧬 #Bioinformatics #Genomics 📄 https://doi.org/10.1093/nar/gkaf1254 👤 EVBC member: Elliot Lefkowitz

raxtax is a fast, k-mer-based taxonomic classifier that matches common k-mers between query and reference sequences, delivering equal accuracy but up to ~100× speed improvements over current tools.🧬⚡#Bioinformatics 📄 https://doi.org/10.1093/bioinformatics/btaf620 👤 EVBC member: Alexandros Stamatakis

KlebPhaCol provides an open, community-driven Klebsiella phage and strain collection spanning five families and a novel phage family, Felixvirales, with data on host range and genome sequences. 🧬🦠 #PhageBiology #OpenResource 📄 https://doi.org/10.1093/nar/gkaf1122 👤 EVBC member: Dimitri Boeckaerts

ICTV’s #VirusTaxonomy database has been significantly enhanced, expanding tools and metadata for virus classification and search, supporting the scientific community with improved access and analytical resources.🧬#Bioinformatics  📄 https://doi.org/10.1093/nar/gkaf1159 👤 EVBC member: Elliot Lefkowitz

Viromics approaches now integrate experimental and computational pipelines to map virus diversity, activity, and host links across microbiomes, enabling large-scale virus ecogenomics. 🧬🔬 #Viromics #Metagenomics  📄 https://doi.org/10.1038/s41576-025-00871-w 👤 EVBC members: Simon Roux

📜 Happy to share the EVBC Newsletter No. 98 for Dec 2025, including the 📝 newest EVBC publications, 🔧 virus bioinformatics tools, 📅 upcoming events, invite to the ViBioM 2026, and 🎤 announcements! evbc.uni-jena.de/evbc-newslet...

📢Join us for the next ECR #Viromics Webinar "Drawing from phage diversity to uncover genomic factors shaping host interaction" ‍🎙️Antônio P. Camargo, Uni São Paulo, Brazil  🗓️10 Dec. 2025, 4 PM CET 📍Online/Zoom (register for login details) 👉 https://evbc.uni-jena.de/events/ecr-viromics-webinar-series/

Host cell-derived Z-RNAs, not viral ones, are the main triggers of ZBP1 activation during HSV-1 and influenza A infection, revealing host defense against viral disruption of transcription termination. #VirusImmunology #CellDeath🧬🦠 📄 https://doi.org/10.1038/s41586-025-08489-2 👤 EVBC: Lars Dölken

High-throughput droplet microfluidics with angle-resolved light scattering imaging and CNN analysis enables multi-antibiotic phenotypic susceptibility results within 3h with 95% categorical agreement to reference methods. #Diagnostics🧬🔬 📄 https://doi.org/10.1016/j.jare.2025.09.047 👤EVBC: Thilo Figge

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

Metagenomic analysis of 101 tomato samples from 13 countries revealed 43 viral species, including PepMV, ToBRFV, and STV, showcasing the global complexity of the commercial tomato virome. #PlantViromics #HTS 🍅🧬 📄 https://doi.org/10.3390/v17101334 👤 EVBC members: Nikolas Basler, Jelle Matthijnssens

VirTrack integrates EBV-host protein-protein interactions with MS clinical type-specific transcriptomes to show how EBV modulates different pathways across CIS, RRMS, SPMS, and PPMS. #SystemsVirology #MultipleSclerosis 🧬 📄 https://doi.org/10.1101/2025.10.05.680499 👤 EVBC: Anna Onisiforou

Study reveals over 3,500 uncharacterized RNA viral RdRp sequences in public protein databases, uncovering many novel endogenous viral elements and misclassified viruses. #VirusEvolution #RNAvirus #Bioinformatics 🧬🧫 📄 https://doi.org/10.1093/ve/veaf074 👤 EVBC members: Andrew Firth, Katherine Brown

Phage-antibiotic synergy reprograms resistance by targeting efflux systems in ESKAPEE pathogens, offering a promising strategy against MDR/XDR bacteria. 🧬🦠  #AntibioticResistance #PhageTherapy #Bacteriophages #MiniReview 📄 https://doi.org/10.1128/mbio.01822-25 👤 EVBC member: Robert Edwards

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

Deep genomic exploration of haloarchaea uncovers complex networks of viruses and virus satellites nested within DPANN symbionts, revealing unexpected layers of microbial interaction. #Viromics #Microbiology #Evolution 🧬🦠 📄 https://doi.org/10.1038/s41564-025-02149-7 👤 EVBC member: Mart Krupovic

Whole-genome sequencing of Lassa virus from dried blood spots proves viable for field settings despite lower RNA yield and coverage compared to whole blood, giving options for virus genome surveillance in remote areas. #ViralGenomics #FieldDiagnostics🦠📦 📄 doi.org/10.1186/s402... 👤 EVBC: Emma Thomson

Novel summary-tree method “HIPSTR” for #Bayesian #phylogenetics shows higher-support clades than MCC trees in Bayesian phylogenetics, for improved computational performance. 📊#bioinformatics #EvolutionaryBiology 📄 https://doi.org/10.1093/bioinformatics/btaf488  👤EVBC: Philippe Lemey, Marc A. Suchard

Using 2 kHz ISCAT #microscopy, this study reveals lipid diffusion in cell #membranes is mostly transiently compartmentalized (100-110 nm domains) with distinct intra- and intercompartmental coefficients. 🔬 📄 https://doi.org/10.1002/cphc.202400407 👤 EVBC: Christian Eggeling

A modeling study of #Ebola outbreaks shows that trade-offs among test accuracy, turnaround time (time-to-isolation), and accessibility can yield greater epidemic reduction when using a rapid, lower-accuracy test than PCR in certain settings.🦠🧪📉 📄 doi.org/10.1186/s128... 👤 EVBC: Isabella Eckerle

Job alert🚨📢! Join us as Director of the SIB Centre for Pathogen Bioinformatics, on a topic where global collaboration is particularly important, in a highly stimulating environment. This is a research infrastructure leadership position. Apply or spread the word! apply.refline.ch/499599/0346/...

CLAE, a high-fidelity nanopore sequencing strategy that achieves Q30 accuracy for up to 27% of reads, recovers novel RNA virus genomes from the environment and SARS-CoV-2 quasi-species in wastewater. #VirusGenomics #Nanopore 🧬 📄 https://doi.org/10.1002/advs.202505978 👤 EVBC member: Matthew Sullivan

Increased COPD severity correlates with lower bacteriophage diversity and viral-bacterial ecological coupling breaks down in frequent exacerbators. #Viromics #RespiratoryMicrobiome 📉🦠 📄 https://doi.org/10.1016/j.celrep.2025.116413 👤 EVBC members: Evelien Adriaenssens, Andrew Millard

New ViralBottleneck R package integrates six methods to estimate viral transmission bottlenecks from deep-sequencing data, revealing how methodological choices shape bottleneck inference. #VirusEvolution #Rstats 🧬 📄 https://doi.org/10.1093/ve/veaf071 👤 EVBC member: Joseph Hughes

📢 Next Viruses in silico lecture: 🎙️ Pathoplexus: A Community-Driven Solution for Transparent and Equitable Viral Genomic Data Sharing 👩‍🔬 Emma Hodcroft @firefoxx66.bsky.social (@swisstph.ch @sib.swiss) 🗓️ 27 Nov 2025 🕑 4 PM CET 📍 Zoom - Register to receive login details 👉 tinyurl.com/VirInSilico

New protocol uses virus-delivered 32nt short RNAs in TRV vector to silence genes in Nicotiana benthamiana, enabling visible phenotype and chlorophyll reduction, facilitating high-throughput functional studies in plants. #PlantViromics🌿🧬 📄 https://doi.org/10.1016/j.xpro.2025.104094 👤EVBC: Fabio Pasin

TRAMbio is a new open‐source Python tool using pebble-game graph rigidity analysis for proteins and macromolecules, enabling rapid detection of rigid/flexible domains in large structures. #Bioinformatics #StructuralBiology 🧬🔧 📄 https://doi.org/10.1186/s12859-025-06300-3 👤 EVBC: Peter F. Stadler

New guidelines for discrete #phylogeography introduce an adjusted Bayes factor (BFₐ𝑑𝑗) that integrates sampling-state abundance, reducing false positives in lineage transition inference under bias. #Phylodynamics #Bioinformatics 🧬📊 📄  https://doi.org/10.1093/molbev/msaf253 👤  EVBC: Simon Dellicour

Metagenomic sequencing in neuroinflammatory disorders uncovers rare viral pathogens and improves diagnostic accuracy, highlighting the value of unbiased viral surveillance in clinical neurology. #VirusDiagnostics #Metagenomics 🧠🧬 📄 doi.org/10.1016/j.di... 👤 EVBC member: Michael Huber

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

Globally traded ornamental aquatic plants host a diverse array of plant viruses, including pathogens relevant to crops, highlighting the hidden risk of virus spread via trade. #PlantViromics #Biosecurity 🌿🦠 📄 doi.org/10.1186/s407... 👤 EVBC member: Denis Kutnjak

A comprehensive survey of GNRA tetraloop-like motifs reveals 12 recurrent backbone topology variants, including pentaloop and multi-strand forms, revealing frequent protein interactions. #MotifDesign #RNAstructure #Bioinformatics 🧬📐 📄 doi.org/10.1038/s415... 👤 EVBC: Janusz Bujnicki

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

📢Join us for the next ECR #Viromics Webinar: "Untangle the complexity of the virosphere using single-cell RNA-sequencing" ‍🎙️ Amir Fromm | Weizmann Institute of Science, Israel 🗓️ 12 November 2025, 4 PM CET 📍 Online | Zoom (register for login details) 👉 coms.osu.edu/webinars/ecr...

Good news! Our website is online again! ✅🥳 🔗 evbc.uni-jena.de We had some technical interruptions over the past weeks due to the relocation of our faculty at FSU Jena. 📦🛠️ Thanks for your patience - and sorry for the inconvenience!

📢 Unfortunately, today's "viruses in silico" talk by Sebastian Böcker has to be cancelled! It will be rescheduled for another date.

📢 Join Us for the Next Viruses in Silico Lecture! 🎙️ SIRIUS and beyond: Turning tandem mass spectra into metabolite structure information 🗓️ 30 October 2025 🕑 4 PM CET 👨‍🔬 Sebastian Böcker (@uni-jena.de) 📍 Zoom - Register to receive the login details 👉 https://tinyurl.com/VirusesInSilico

Nature research paper: Isolation, engineering and ecology of temperate phages from the human gut go.nature.com/4hmvWLh

📢 Join Us for the Next Viruses in Silico Lecture! 🎙️ SIRIUS and beyond: Turning tandem mass spectra into metabolite structure information 🗓️ 30 October 2025 🕑 4 PM CET 👨‍🔬 Sebastian Böcker (@uni-jena.de) 📍 Zoom - Register to receive the login details 👉 https://tinyurl.com/VirusesInSilico

HIV-phyloTSI uses diversity (MAF) and divergence (LRTT) metrics from deep #HIV-1 sequencing to produce continuous, subtype-independent estimates of time since infection, enabling incidence estimation with <12mo MAE and robust performance 📄https://doi.org/10.1186/s12859-025-06189-y 👤EVBC: Astrid Gall

A nationwide #HTS survey of German hopyards identified HpLV, HpMV, ApMV, ArMV and viroids HLVd and CBCVd (CBCVd confined to Hallertau), highlighting HTS as a powerful tool for #PlantPathogenSurveillance and management #PlantViromics 🧬🌾🔬 📄https://doi.org/10.1371/journal.pone.0329289 👤EVBC: Ali Pasha

📢Join us for the next ECR #Viromics Webinar: "Characterising novel viral proteins using protein language models (PLMs)" ‍🎙️ Kieran Lamb (@kieranlamb.bsky.social) | University of Glasgow/UK 🗓️ 8 October 2025, 4 PM CEST 📍 Online | Zoom (register for login details) 👉 coms.osu.edu/webinars/ecr...