📢 Poster submission for ViBioM 2026 closes soon!
Present your work and connect with the #virology & #bioinformatics community in Vilnius.
📜 Deadline: 17 April 2026, 23:59 CEST
🔗 evbc.uni-jena.de/events/vibiom2026/confer...
#ViBioM2026 #ComputationalBiology

The making and breaking of insect endogenous retroviruses - The EMBO Journal The EMBO Journal - Retroelements are main constituents of eukaryotic genomes. Recent work by Senti et al (2025) reports that retrotransposons and endogenous retroviruses occupy specific...

Endogenous #retroviruses in insects evolve via gain and loss of infectivity, shaping distinct cellular niches and host interactions. A compelling perspective on virus–host #coevolution in #Drosophila.🧬🦠#Virology #TransposableElements
📄https://doi.org/10.1038/s44318-025-00472-7
👤EVBC: Ronald van Rij

From Heatwaves to Brainwaves: Climate-Driven Microplastics Promote Epstein–Barr Virus Reactivation and Female-Biased Risk for Alzheimer’s Disease and Multiple Sclerosis Background Climate change accelerates plastic degradation, increasing human exposure to microplastics and their associated endocrine-disrupting additives, thereby reshaping the chemical exposome. Many of these compounds, including bisphenols and phthalates, act as xenoestrogens capabl...

Climate‑driven #microplastic exposure may intersect with Epstein–Barr virus biology and endocrine pathways, potentially increasing female‑biased risk for Alzheimer’s and MS. 🌍🦠#EBV #Exposome #ClimateChange #Neurodegeneration
📄https://doi.org/10.21203/rs.3.rs-8928857/v1
👤EVBC member: Anna Onisiforou

📢 Join Us for the Next Viruses in silico Lecture!
🎙️ Influenza and SARS-CoV-2: from evolutionary predictions to prospective vaccination
🗓️ 30 April 2026 🕑 4 PM CEST
👨‍🔬 Michael Lässig (University of Cologne, Germany)
📍 Zoom - Register to receive the login details
👉 evbc.uni-jena.de/events/virus...

Picobirnavirus: how do you find where it’s hiding? Picobirnaviruses (PBVs) are double-stranded RNA viruses detected in various environments and host-associated samples, including those from humans, non-human animals, invertebrates and birds. First ...

Picobirnaviruses remain elusive, with unclear hosts and detection challenges. This review evaluates PCR, #metagenomics, and host inference strategies to clarify their biology and ecology.🔬🧬#Virology #RNAviruses #Bioinformatics
📄https://doi.org/10.1080/1040841X.2025.2560918
👤EVBC: Robert Edwards

Multiple origins and functions: evolutionary pathways of HSP70 proteins in viruses Heat shock protein 70s (HSP70s) are highly conserved molecular chaperones found across all domains of life, where they play essential roles in cellular stress responses. Whilst HSP70 homologues have been previously identified in closteroviruses that have ssRNA genomes, their broader presence and evolutionary history in viruses remain poorly understood. In this study, we conducted a comprehensive search of viral protein databases and identified HSP70 homologues in viruses beyond those with ssRNA genomes, including examples with dsDNA genomes in the class Megaviricete. These viral HSP70s exhibit diverse gene organizations, copy numbers and structural features. Notably, HSP70s of viruses from Megaviricetes showed up to three gene copies per genome and distinct structural motifs, whilst those from closteroviruses displayed higher sequence and structural diversity, suggesting faster evolutionary rates. Structural and phylogenetic analyses revealed two major clusters of viral HSP70s, with dsDNA virus HSP70s closely resembling those of their protist hosts, supporting the hypothesis of horizontal gene transfer. In contrast, ssRNA virus HSP70s formed a distinct, highly divergent group. Our findings suggest multiple independent acquisitions of HSP70 genes by viruses and provide new insights into their evolutionary trajectories and potential functional adaptations.

Virus HSP70s show multiple independent origins, with distinct evolutionary paths in ssRNA and dsDNA viruses, highlighting #HorizontalGeneTransfer and functional diversification.🧬🔥#Virology #Evolution #HSP70 #MolecularEvolution
📄https://doi.org/10.1099/jgv.0.002242
👤EVBC: Santiago F. Elena

Phage–antibiotic synergy restores β-lactam efficacy in MDR Klebsiella quasipneumoniae biofilms and suppresses resistance - Journal of Biomedical Science Background Biofilms formed by multidrug-resistant (MDR) Klebsiella spp. present a significant clinical challenge due to elevated antibiotic tolerance. Bacteriophages (phages) represent a promising alternative, particularly in combination with antibiotics, where phage–antibiotic synergy (PAS) can increase antibiofilm activity. Evaluating treatment efficacy in these complex structures requires real-time, noninvasive viability analysis. Methods To address this, we used light-sheet fluorescence microscopy (LSFM), a high-resolution, minimally invasive approach, for dynamic tracking of PAS in intact biofilms. To our knowledge, this is the first in vitro application of LSFM for investigating PAS. We studied the combined activity of a virulent phage (vB_KpUKJ_2) and ceftazidime (CAZ) against an extended-spectrum β-lactamase-producing Klebsiella quasipneumoniae. Results In planktonic cultures, PAS was strongly affected in a dose-dependent manner. In mature biofilms, LSFM imaging revealed that high-dose phages (10⁸ PFU/mL) combined with CAZ at a 0.25 × minimum inhibitory concentration (MIC) induced a rapid and sustained reduction in viability over 24 h. This regimen significantly outperformed mono-treatments (p < 0.01), demonstrating that phage coadministration can reduce the required antibiotic dose. Mechanistically, treatment resulted in phage-mediated degradation of α- and β-polysaccharides within the extracellular polymeric substance (EPS). Crucially, while phage mono-treatment led to the emergence of resistant mutants, the combination treatment fully suppressed resistance. Whole-genome sequencing revealed mutations in genes such as fhuA, purA, and rpoC, suggesting diverse resistance mechanisms linked to fitness trade-offs such as impaired biofilm formation. Conclusions Our findings highlight a precision-guided strategy with translational potential for device-associated infections, providing a mechanistic and methodological foundation for optimizing PAS-based therapies.

Phage–antibiotic synergy restores β-lactam activity against MDR Klebsiella #biofilms and limits resistance emergence, highlighting a promising strategy to combat antimicrobial resistance.🦠💊#AMR #Microbiology
📄https://doi.org/10.1186/s12929-026-01218-1
👤EVBC: Mike Marquet, Ralf Ehricht, Mathias Pletz

Ordinary differential equation models of SARS-CoV-2 replication dynamics and antiviral drug efficacies - npj Viruses npj Viruses - Ordinary differential equation models of SARS-CoV-2 replication dynamics and antiviral drug efficacies

New review examines how target-cell-limited ordinary differential equation models of #SARSCoV2 replication help quantify virus dynamics + antiviral drug effects in vitro⚙️🦠🔬🧫💊#MathematicalModeling #AntiviralTherapy #ComputationalBiology
📄https://doi.org/10.1038/s44298-026-00183-8
👤EVBC: Lars Kaderali

Lassa Virus Live Tracking and Lineage Assignment: How Nextstrain Can Enhance Surveillance and Public Health in Africa and Beyond Lassa virus (LASV), a zoonotic, bi-segmented arenavirus endemic to West Africa, causes seasonal epidemics with substantial morbidity and mortality. Increasing frequency of exported cases emphasises...

New article shows how #Nextstrain based live tracking and lineage assignment for #LassaVirus can strengthen #GenomicSurveillance and #PublicHealth response in Africa and beyond 🔬🦠🌍 #Virology
📄 https://doi.org/10.1080/22221751.2026.2640699
👤 EVBC: Knut Reinert, Denise Kühnert

The Immunosuppression Paradox in Multiple Sclerosis: Are We Fueling the Fire by Suppressing Immunity in an Epstein–Barr Virus–Linked Disease? Abstract. Recent studies strongly implicate Epstein–Barr virus (EBV) as a necessary trigger for multiple sclerosis (MS). Longitudinal data show that EBV se

This review explores the paradox of using immunosuppression to treat Epstein–Barr virus–linked multiple sclerosis, suggesting future strategies may need EBV targeted therapies.🧠🦠 #MultipleSclerosis #EBV #Immunology #Neurovirology #Autoimmunity
📄 doi.org/10.1093/ofid...
👤 EVBC member: Anna Onisiforou

Happy to share EVBC Newsletter No. 101 (March 2026) including:
📢 Info on ViBioM 2026
📜 Newest EVBC member publications
📅 Upcoming events
💼 Open vacancies
🎤 Webinar announcements
🔗 https://evbc.uni-jena.de/evbc-newsletter/
#bioinformatics #virology

Addressing pandemic-wide systematic errors in the SARS-CoV-2 phylogeny - Nature Methods This Resource paper presents a global SARS-CoV-2 phylogenetic tree of 4,471,579 high-quality genomes consistently constructed by Viridian, an efficient amplicon-aware assembler.

A new resource re-assembles millions of SARS-CoV-2 #genomes using an amplicon aware pipeline (Viridian) to remove systematic sequencing errors and provide a high quality global #phylogeny of 4.47M samples 🧬🌍
📄 https://doi.org/10.1038/s41592-025-02947-1
👤 EVBC members: Martin Hölzer, Marie Lataretu

Comprehensive guide to maximise #nanopore #sequencing performance, covering experimental optimisation and advanced computational analysis to unlock richer #genomic and transcriptomic insights🧬🔬
📄 https://doi.org/10.1093/nar/gkag023
👤 EVBC: Sebastian Krautwurst, Martin Hölzer, Jörg Linde, Manja Marz

🎉 Registration for ECCB 2026 is now open!
Join the computational biology community in Geneva for 5 days of science & collaboration. Organized by the @sib.swiss Institute of Bioinformatics.
⏰ Early bird until 31 March
📆 31 Aug - 4 Sep 2026
👉 eccb2026.org/registration...
#eccb2026 #GenevaLovesData

Frontiers | Diversity of DNA viruses in the atmosphere of sub-Antarctic South Georgia Studying airborne viruses in remote environments like the sub-Antarctic island of South Georgia offers key insights into viral ecology, diversity, and their ...

Airborne DNA virus communities over sub Antarctic South Georgia show unexpected diversity and oceanic links, with many virus sequences related to marine phages and extremophile associated viruses. 🌊🦠#Virology #Metagenomics
📄 https://doi.org/10.3389/fmicb.2025.1726848
👤 EVBC member: Janina Rahlff

🤝 Meet the EVBC at #GfV2026 in Heidelberg!
Stop by our poster “Ten Years at the Interface of Viruses and Data – The European Virus Bioinformatics Center” to learn more about EVBC and virus bioinformatics collaborations!
🗓️ 19 March, 3–5 pm
📍 Poster P513, Poster exhibition 4
#virology #bioinformatics

🧑‍💻Satellite Hackathon at #ViBioM2026!
Join the Virus #Bioinformatics + nf-core Hybrid Collaborative #Hackathon and collaborate on bioinformatic tools and ideas and contribute to reproducible workflows and research infrastructure.
🔗 evbc.uni-jena.de/events/vibiom2026/hackat...

New #groundwater #microbiome research from the Slovenian Dinaric #Karst reveals diversity of viruses, bacteria, and fungi across karst aquifers, expanding understanding of subterranean #biodiversity and ecosystem processes🧬💧
📄 https://doi.org/10.1016/j.ecoenv.2026.119890
👤 EVBC: Denis Kutnjak

📢 Registration for ViBioM 2026 is now open!
Join us in Vilnius this May for ViBioM 2026 and connect with researchers working at the intersection of virology and bioinformatics.
🗓️ Registration deadline: 30 April
🔗 evbc.uni-jena.de/events/vibio...
#ViBioM2026 #virology #bioinformatics

CRESSENT: a bioinformatics toolkit to explore and improve ssDNA virus annotation ssDNA viruses are important components of diverse ecosystems; however, it remains challenging to systematically identify and classify them. This is partly due to their broad host range and resulting genomic diversity, structure and rapid evolutionary rates. In addition, distinguishing genuine ssDNA genomes from contaminating sequences in metagenomic datasets (e.g. from commercial kits) has been an unresolved issue for years. Here, we present CRESSENT (CRESS-DNA Extended aNnotation Toolkit), a comprehensive and modular bioinformatic pipeline focused on ssDNA virus ‘genome-to-analysis’ and annotation. The pipeline integrates multiple functionalities organized into several modules: sequence dereplication, decontamination, phylogenetic analysis, motif discovery, stem-loop structure prediction and recombination detection. Each module can be used independently or in combination with others, allowing researchers to customize their analysis workflow. With this tool, researchers can comprehensively and systematically include ssDNA viruses in their viromics workflows and facilitate comparative genomic studies, which are often limited to dsDNA viruses, therefore leaving behind a crucial component of the microbiome community under study. Benchmarking analyses demonstrated that CRESSENT efficiently processes ssDNA virus datasets of varying scales, completing small family-level analyses within minutes and moderate comparative genomics studies within hours using standard computing resources. Its modular, parallelized design ensures scalability and low memory usage, making it accessible to research groups with diverse computational capacities.

🔬 New #ssDNA virus annotation toolkit CRESSENT accelerates #viromics & ecosystem virus discovery with modular, scalable analyses for decontamination, structuring & phylogeny. 🧬💻#Virology #Bioinformatics #Metagenomics
📄 https://doi.org/10.1099/mgen.0.001632
👤 EVBC member: Matthew Sullivan

Bacteriophages exploit lateral transduction to mobilize bacterial antiphage defense systems, reshaping how immune genes spread and influence pathogen evolution. 🦠🔁#Microbiology #Bacteriophage #HorizontalGeneTransfer #Evolution
📄 https://doi.org/10.1126/sciadv.adx5749
👤 EVBC member: José R. Penadés

New study shows that virus prevalence in multispecies #BeeCommunities is shaped by the identity of key host species and the structure of their interaction networks, with implications for #DiseaseEcology. 🐝🦠#Ecology #NetworkScience
📄 https://doi.org/10.1111/ele.70327
👤 EVBC member: Robert Paxton

⏰Abstract submission for #ViBioM2026 is open until midnight tonight (00:00 CET) - Don't miss your chance to present a talk at the International Virus Bioinformatics Meeting! 🎤🦠🧬💻
👉 evbc.uni-jena.de/events/vibio...
#virology #bioinformatics

Tracking SARS-CoV-2 genomic variants in wastewater sequencing data with LolliPop Author summary Wastewater-based epidemiology has become a valuable tool for tracking viruses like SARS-CoV-2 across entire communities. Sequencing wastewater can reveal which viral variants are circulating, offering early insights into variant dynamics while avoiding the biases of clinical testing. A central challenge is to infer the relative abundances of these variants from observed mutation data. This task is complicated by the fact that variant profiles can be highly similar, and the data is often noisy with many missing read count values from genomic positions with no coverage, especially when the incidence of the pathogen is low. We developed LolliPop, a statistical method that leverages the time series structure of wastewater data to robustly deconvolve variant abundances and compute fast confidence intervals. Using both simulated data and real data from the Swiss national variant monitoring, we show that LolliPop is accurate and robust to high levels of missing data.

LolliPop enables accurate deconvolution of SARS-CoV-2 variants from wastewater sequencing, strengthening genomic surveillance and early outbreak detection. 🧬🚰 #WastewaterEpidemiology #COVID19 #Bioinformatics
📄 https://doi.org/10.1371/journal.pcbi.1014003
👤 EVBC member: Niko Beerenwinkel

Community-acquired pneumonia in diabetic patients is characterised by a distinct pathogen spectrum and enhanced inflammation: results from CAPNETZ, a prospective observational cohort study - Infection Purpose Diabetes mellitus (DM) is a relevant risk factor for enhanced susceptibility to and adverse outcomes in infections, including community-acquired pneumonia (CAP). We aimed to characterise clinical outcomes, inflammatory and organ failure markers and microbial etiologies in diabetic (DM+) versus non-diabetic (DM−) patients in a European CAP cohort. Methods Comparative analyses using data from the CAPNETZ multicenter, prospective, observational study including 13,611 patients with CAP enrolled between 2002–2022, with and without a history of DM, were conducted. Results Seventeen percent (2310/13,611) had a history of DM (DM+). Compared to DM− patients, DM+ patients had a higher 180 days mortality rate following CAP (13% (292/2310) vs. 7% (766/11,301), p < 0.0001) and higher C-reactive protein and leucocyte counts (median CRP 97 mg/L (IQR: 31–202) vs. 86 mg/L (IQR: 24–190), p < 0.0001; median leucocyte count 12/nl (IQR: 9–16)vs. 11/nl (IQR: 8–15), p < 0.0001). Pathogens were identified in 23.4% (540/2310) of the DM+ and 21.7% (2414/11,301) of the DM− patients (p = 0.03), respectively. Overall, pathogen distribution differed between the two groups, with higher frequencies of Enterobacteriaceae in the DM+ group (13.0% (70/539) vs. 8.0% (194/2414), padj < 0.01). Conclusions CAP in DM+ is characterised by a distinct microbial spectrum and enhanced inflammation. While further studies are needed to elucidate the clinical impact of our findings, we recommend early and comprehensive CAP pathogen testing in DM+ patients.

Prospective cohort data from over 13,600 CAP patients show that individuals with #diabetes have a distinct #pathogen spectrum, heightened inflammatory responses, and worse outcomes compared to non diabetic patients. 💉📊 #Pneumonia
📄 https://doi.org/10.1007/s15010-025-02659-w
👤 EVBC: Mathias Pletz

📢Join us for the next ECR #Viromics Webinar
"Scalable annotation and curation of auxiliary viral genes with CheckAMG"
‍🎙️James Kosmopoulos, Anantharaman Lab, University of Wisconsin-Madison, USA
🗓️11 March 2026, 4 PM CET
📍Online/Zoom (register for login details)
👉 evbc.uni-jena.de/events/ecr-v...

First full-genome alignment representative for the genus Pestivirus A monthly journal publishing high-quality, peer-reviewed research on all topics related to RNA and its metabolism in all organisms

First full genome multiple sequence alignment for the genus #Pestivirus reveals conserved #RNA structures and phylogenetic patterns across all known species, providing a key resource for #virus RNA analysis🧬
📄 www.rnajournal.org/cgi/doi/10.1261/rna.0807...
👤EVBC: Sandra Triebel, Manja Marz

TEvarSim: A genome simulator for transposable element (TE) variants Author summary TEvarSim is the first all-in-one toolkit that generates transposable element (TE) variant-carrying genomes, sequencing reads, and VCF files, and directly compares simulated and predicted TE variants, providing a comprehensive solution for benchmarking TE detection and genotyping. It is the first simulator to incorporate real TE sequences, extract TEs from pangenome graphs, and introduce natural sequence variation across genomes, supporting biologically relevant TE research. TEvarSim is also the first to directly and automatically simulate both TE insertions and deletions, providing a better understanding of the full spectrum of TE polymorphisms. TEvarSim can rapidly simulate thousands of individual synthetic genomes containing TE variants.

TEvarSim introduces an integrated simulator for transposable element variants, enabling robust benchmarking and evaluation of TE detection tools across genomes. 🧬⚙️ #Bioinformatics #Genomics #TransposableElements
📄 https://doi.org/10.1371/journal.pcbi.1013933
👤 EVBC member: Dawei Li

📢 Submit your abstract for ViBioM 2026 in Vilnius!!
Share your work and be part of the International Virus Bioinformatics Meeting on 18-20 May!
#virology #bioinformatics #ViBioM2026
🎤 Talk Abstract Deadline: 6 March 2026
📜 Poster Title Deadline: 17 April 2026
🔗 evbc.uni-jena.de/events/vibio...

🎉 Delighted to share the 100th EVBC Newsletter of February 2026, featuring the 📝 newest EVBC publications, 🔎 job vacancies, 🔧 virus bioinformatics tools, 📅 upcoming events, and info for ViBioM 2026!
🔗 evbc.uni-jena.de/evbc-newslet...