European Virus Bioinformatics Center

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🧬
📄 http://www.rnajournal.org/cgi/doi/10.1261/rna.080732.125
👤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...

📢 Join Us for the Next Viruses in silico Lecture!
🎙️ SIRIUS and beyond: Turning tandem mass spectra into metabolite structure information
🗓️ 26 February 2026 🕑 4 PM CET
👨‍🔬 Sebastian Böcker (@uni-jena.de)
📍 Zoom - Register to receive the login details
👉 https://evbc.uni-jena.de/events/viruses-in-silico/

A new NAR Genomics and Bioinformatics resource introduces SquiDBase, a community repository of raw #nanopore #microbiome sequencing data, supporting open access and broader utility for bioinformatics and comparative analyses. #Genomics
📄 https://doi.org/10.1093/nargab/lqaf213
👤 EVBC: Daan Jansen

Defining expansions and perturbations to the RNA polymerase III transcriptome and epitranscriptome by modified direct RNA nanopore sequencing - Nature Communications RNA polymerase III transcribes essential non-coding RNAs, but many aspects of this biology remain unclear. Here, the authors develop DRAP3R, a nanopore sequencing method that captures Pol III transcripts and RNA modifications, revealing new RNAs and dynamic modification patterns.

New paper uses a modified direct #RNA #nanopore sequencing framework (DRAP3R) to reveal expanded RNA polymerase III #transcriptome and epitranscriptome landscapes, including novel Pol III-transcribed RNAs. 🧬
📄 https://doi.org/10.1038/s41467-025-68230-1
👤 EVBC member: Daniel Depledge

Viral entry shapes HCMV latency establishment - Nature Communications HCMV infection can become productive or latent. Here the authors show that variations in the number of incoming viral particles across cell types is a key factor of this decision, identifying entry efficiency as a key regulator of latency.

New study shows that inefficient virus entry into monocytes partly drives establishment of #HCMV #latency, with integrin β3 identified as a key entry factor modulating productive versus latent infection. #virology
📄 https://doi.org/10.1038/s41467-025-68063-y
👤 EVBC member: Noam Stern Ginossar

SIMPLICITY is an agent-based, multi-scale mathematical model to study SARS-CoV-2 intra- and between-host evolution - Communications Biology SIMPLICITY models multi-scale SARS-CoV-2 evolution by integrating within-host viral dynamics and population-level transmission. Our adaptive fitness landscape model reveals how immune escape prompts evolutionary dynamics akin to the real-world evolution of SARS-CoV-2.

New paper introduces SIMPLICITY, a multi scale agent based model linking within host virus evolution and population spread to dissect SARS-CoV-2 evolutionary dynamics.📊🦠#Epidemiology #Modeling #VirusEvolution
📄 https://doi.org/10.1038/s42003-025-09403-y
👤 EVBC members: Denise Kühnert, Max von Kleist

📢 Join Us for the Next Viruses in silico Lecture!
🎙️ SIRIUS and beyond: Turning tandem mass spectra into metabolite structure information
🗓️ 26 February 2026 🕑 4 PM CET
👨‍🔬 Sebastian Böcker (@uni-jena.de)
📍 Zoom - Register to receive the login details
👉 https://evbc.uni-jena.de/events/viruses-in-silico/

Newly developed #iPSC-derived human alveolar type II model supports productive influenza A virus infection and #antiviral testing and offers a scalable platform for #Influenza research and drug evaluation.
📄 https://doi.org/10.1002/adhm.202405141
👤 EVBC: Marc Thilo Figge, Christian Eggeling

RNA virus genomes from centuries- to millennia-old Adélie penguin mummies Direct studies of long-term RNA virus evolution are largely limited to chemically-fixed specimens from natural history and pathology museums collected over the past two centuries. Detecting genomic traces of RNA viruses in older, buried remains is generally considered highly unlikely. The cold, dry conditions of Antarctica may represent an exception. Under such circumstances, natural mummification of penguins and seals—animals that form large colonies where RNA viruses circulate—is common and may facilitate the recovery of RNA virus genomes. Here, we show that Adélie penguin ( Pygoscelis adeliae ) mummies, ranging in age from recent to nearly two millennia, indeed contain fragments of such ancient viral genomes. Metatranscriptomic analyses yielded near-complete genome sequences of a picornavirus ( Megrivirus epengu ) and a rotavirus D ( Rotavirus deltagastroenteritidis ) from relatively recent specimens. We further retrieved rotavirus D sequences from a 280-year-old individual and a near-complete rotavirus G ( Rotavirus gammagastroenteritidis ) genome from a 1900-year-old one. These findings pave the way to direct studies of RNA virus evolution across millennia. ### Competing Interest Statement The authors have declared no competing interest. Deutsche Forschungsgemeinschaft (DFG, German Research Foundation), Transregio Collaborative Research Centre 410 “WETSCAPES2.0”, Project-ID 531801029 – TRR 410 National Science Foundation, ANT 1443386, OPP 9909274 US National Institutes of Health, R01 AI153044 Research Foundation - Flanders (‘Fonds voor Wetenschappelijk Onderzoek - Vlaanderen’, G0D5117N, G0B9317N, G051322N Deutsche Forschungsgemeinschaft (DFG, German Research Foundation), Germany's Excellence Strategy - EXC 2155 - project number 390874280 Helmholtz Association’s Initiative and Network Fund, KA1-Co-02 “CoViPa”

Preprint reveals that centuries-/millennia-old Adelie penguin mummies preserve near-complete RNA virus genomes, enabling the study of long-term #RNA #virus #evolution in Antarctic remains.🧬❄️
📄 https://doi.org/10.64898/2025.12.17.693957
👤 EVBC: C. Lauber, M. A. Suchard, P. Lemey, S. Calvignac-Spencer

📢Join us for the next ECR #Viromics Webinar
"How viral evolution is shaped during long-term infections of immune-compromised hosts"
‍🎙️Jonas Fuchs, University Hospital Freiburg, Germany
🗓️11 Feb 2026, 4 PM CET
📍Online/Zoom (register for login details)
👉 evbc.uni-jena.de/events/ecr-v...

New review highlights how #MachineLearning and #ArtificialIntelligence models are transforming mitotic checkpoint modelling, from predictive biology to clinical precision medicine. 🤖🧬⚕️ #CellBiology #Bioinformatics
📄 https://doi.org/10.1093/bib/bbaf729
👤 EVBC member: Bashar Ibrahim

New study reveals how glycyl-tRNA synthetase binding boosts Mengovirus RNA #translation, offering fresh insights into RNA–protein interactions and virus gene expression. 📈#Virology #RNAbiology
📄 https://doi.org/10.1093/nar/gkaf1451
👤 EVBC: Markus Fricke, Muriel Ritsch, Manja Marz, Michael Niepmann

This paper presents torchtree, a flexible Python/PyTorch framework for #phylogenetic model development and inference using variational Bayes and other gradient-based methods. 🚀🌳 #BayesianInference #PyTorch #Bioinformatics
📄 https://doi.org/10.1093/sysbio/syaf047
👤 EVBC member: Marc A. Suchard

Extended poly(A) tails are a shared feature of herpesvirus mRNAs Poly(A) tails are present on most cellular and viral mRNAs, providing a platform for poly(A)-binding proteins that stimulate translation and regulate the deadenylation and stability of transcripts in the cytoplasm. Here we leverage nanopore direct RNA sequencing to analyse the distribution of poly(A) tail lengths on cellular and viral mRNAs across Herpesviridae and other DNA and RNA virus infections. We find that herpesvirus mRNA poly(A) tails are consistently longer than those on cellular and other viral transcripts, presenting a previously unrecognized yet widespread mechanism to advantage herpesviral gene expression. This contrasts with the templated poly(A) tails on coronavirus RNAs and those on cytoplasmically transcribed poxviral mRNAs, which are more similar in length to those on host mRNAs. Herpesviral noncoding RNAs display differential poly(A) tailing patterns which do not correlate with nuclear localisation while individual herpesviral mRNAs also show variation in the extent to which their poly(A) tail lengths change during the virus lifecycle, suggestive of additional uncharacterised layers of poly(A) tail length regulation. Importantly, while we detect non-adenosine nucleotides within herpesviral poly(A) tails, which are known to oppose deadenylase activity, this “mixed tailing” is not at sufficient frequency to explain the widespread extended tails of herpesvirus mRNAs. ### Competing Interest Statement The authors have declared no competing interest.

New preprint finds extended poly(A) tails are a shared feature of #herpesvirus mRNAs, suggesting conserved post-transcriptional regulation across herpesviruses and potential impacts on translation and stability. 🧬📄 #Virology
📄 https://doi.org/10.64898/2025.12.15.694445
👤 EVBC member: Daniel Depledge

Two-year persistence of MERS-CoV-specific antibody and T cell responses after MVA-MERS-S vaccination in healthy adults - Nature Communications This study assessed the&nbsp;durability of immunity&nbsp;in humans after vaccination with an MVA-based MERS&nbsp;vaccine. The data show that antibodies and T&nbsp;cells persist for at least two years, with the&nbsp;antibodies capable of cross-neutralizing MERS-CoV variants.

Two year persistence of #MERS CoV specific antibody and T cell responses after three doses of the MVA MERS S #vaccine in healthy adults shows durable humoral and cellular immunity. 💉🧬#Immunology
📄 https://doi.org/10.1038/s41467-025-68248-5
👤 EVBC members: Christian Drosten, Stephan Becker

Introducing ViMOP, a user friendly #nanopore sequencing pipeline for untargeted #VirusGenome assembly that works with clinical and field data to deliver high quality consensus genomes with minimal setup.🦠🔬 #Bioinformatics
📄 https://doi.org/10.1093/bioinformatics/btaf687
👤 EVBC member: Philippe Lemey

The Nucleic Acids Circular Dichroism and Fourier Transform Databases NACDDB and NAIRDB: New Tools for RNA Structural Analysis Fourier Transform Infrared (FTIR) and Circular Dichroism (CD) spectroscopies are powerful and rapid techniques that provide valuable insights into the conformational properties of nucleic acids&#160;(NA). These spectroscopic methods, sensitive to vibrational and...

New protocol introduces NACDDB and NAIRDB: web-accessible circular dichroism and Fourier transform #databases for #RNA structural analysis, empowering spectroscopic interpretation and comparative studies. 🔬🧬 #Spectroscopy
📄 https://doi.org/10.1007/978-1-0716-5084-4_4
👤 EVBC member: Janusz Bujnicki

Transcriptome mining reveals diversity and evolution of circulating and endogenous amphibian retroviruses - Retrovirology Background The evolutionary history of retroviruses and their impact on vertebrate evolution remains poorly understood, particularly in non-mammalian hosts. In this study, we explore retroviruses associated with Amphibia through analysis of 169 RNA sequencing datasets from 102 amphibian species. Using a BLAST-based approach, we identified retroviral transcripts from assembled transcriptomes and phylogenetically characterise both their pol and env regions to elucidate their evolutionary history. Results We identified the transcription of 18 novel and two previously described retroviruses with closest relatives in gammaretrovirus, epsilonretrovirus, betaretrovirus and spumaretrovirinae. Despite their differing pol phylogenies, we found that all amphibian retroviruses belong to the gamma-type envelope group (GTE). This suggests a common selection pressure for amphibian retroviruses to retain GTEs. Within these GTEs we also observed a new clade of alpharetrovirus-like envelopes in amphibians which form a sister clade to avian alpharetrovirus envelopes. Furthermore, we observe correlations between amphibian taxonomical order and retroviral diversity, with Gymnophiona (caecilians) harbouring the widest diversity of retroviruses whilst Anura (frogs and toads) harbour the fewest. Through mapping these transcribed retroviruses to their respective genomes (seven available) supplemented with observing ORF intactness, we determined that 14 of the 20 retroviruses are likely endogenous in origin yet are still transcribed in many amphibian tissues. These amphibian endogenous retroviruses (ERVs) have high genomic copy numbers: most (5/7) ERVs investigated have > 100 copies, and one of which has 9,219 integrations within the Ichthyophis bannanicus caecilian genome. This high retroviral load in amphibian genomes may suggest that these retroviruses have low pathogenicity, or may reflect a lack of transposon control mechanisms in amphibian cells. Conclusions Through the characterisation of metatranscriptomic and genomic data from retroviruses in this study, we provide insights into their evolution in amphibians and exemplify the diversity of Retroviridae in vertebrate genomes. The identification of novel retroviral clades, widespread transcription of endogenous retroviruses in amphibians and abundance of ERV copies suggests that Retroviridae have played a significant role in amphibian evolution.

New study uncovers extensive diversity of circulating and endogenous #amphibian #retroviruses, identifying 20 retrovirus transcripts across 102 species, revealing deep evolutionary patterns in vertebrate hosts.🦎🧬#VirusEvolution
📄 https://doi.org/10.1186/s12977-025-00669-y
👤 EVBC member: Emma Harding