European Virus Bioinformatics Center

European Virus Bioinformatics Center

@evbc.bsky.social

Bringing together the excellence of virology and bioinformatics. Tools: http://bit.ly/evbctools Impressum: https://evbc.uni-jena.de/impressum/

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Metagenomics of three rural #groundwater pumps in Egypt recovered 9,534 virus contigs, revealing site-specific viromes dominated by novel bacteriophages with potential roles in microbial ecology and metabolism ๐Ÿงฌ๐Ÿ’ง #Viromics ๐Ÿ“„ https://doi.org/10.1007/s00248-026-02818-y ๐Ÿ‘ค EVBC member: Ali Elbehery

doi.orgMetagenomic Analysis of Rural Groundwater Viromes Reveals Bacteriophage Contributions to Groundwater Microbial Ecology - Microbial EcologyGroundwater ecosystems host diverse microbial communities, yet the diversity and ecological roles of their associated viral genomes remain poorly characterized. Here, we investigated viral community composition, diversity, host associations, lifestyles, and auxiliary metabolic potential in groundwater from three hand pumps located in Toukh, Qalyubia, Egypt, representing distinct local surroundings and potential contamination pressures. Using complementary viral detection approaches and a quality assessment workflow, we recovered 9,534 non-redundant viral contigs spanning a wide range of viral genome quality. Taxonomic profiling revealed dominance of tailed dsDNA bacteriophages (Uroviricota/Caudoviricetes) across all pumps, with ~โ€‰99% of contigs not assigned below the class level. Whereas the viral composition of pump 3 was distinct and its diversity was consistently higher, pumps 1 and 2 clustered together, a pattern mirrored across taxonomic scales and diversity metrics. The majority of predicted viral hosts belonged to phylum Pseudomonadota, followed by Actinomycetota, Bacillota and Bacteroidota, with levels that varied between pumps. Correlation and network analyses showed strong concordance between the relative abundance of bacteria and the abundance of viruses that potentially infect them. Lifestyle prediction indicated a descending relative abundance of viruses with lysogenic lifestyle from pumps 1 through 3. Auxiliary metabolic genes (AMGs) related mainly to nucleotide, amino acid, and cofactor metabolism were detected in all pumps, with distinct pump-specific repertoires suggesting localized viral metabolic strategies. Together, these results demonstrate that groundwater viromes are ecologically structured and highly novel, with the potential ability to modulate host metabolism, highlighting their potential role in shaping subsurface microbial communities.

New protocol combines sequence homology, protein structures, genome synteny & protein language models to annotate metagenomic prokaryotic viruses. Pharokka, Phold and Phynteny help uncover viral dark matter and visualise genome features๐Ÿฆ ๐Ÿ”ฌ ๐Ÿ“„ https://doi.org/10.1002/cpz1.70405 ๐Ÿ‘คEVBC: Robert J. Edwards

doi.orgDecoding Viral Dark Matter: Metagenomic Prokaryotic Virus Characterization With Pharokka, Phold, and PhyntenyViral metagenomics is an increasingly powerful tool for understanding the function and structure of viruses across the diverse environments of our planet. However, decoding the functional potential o...

A review traces #VirusDiscovery from classical assays to metagenomics and AI, highlighting protein-structure comparison as a promising route beyond sequence similarity and viral dark matter ๐Ÿงฌ๐Ÿค– #Viromics ๐Ÿ“„ https://doi.org/10.1099/mgen.0.001785 ๐Ÿ‘ค EVBC: Amanda Araujo Serrao de Andrade, Ann C. Gregory

doi.orgEvolving strategies for virus discoveryViruses interact with all domains of life and play fundamental roles in shaping biological systems from individual hosts to global ecosystems. Yet their identification remains difficult due to a lack of a universal marker gene and the extensive diversity of viral genomes. Despite this, the speed of...

New tool ConvMut maps recurring SARS-CoV-2 mutations across PANGO-based phylogenies, helping researchers track immune escape and inform vaccine and antibody design ๐Ÿงฌ๐Ÿฆ  #SARSCoV2 #VirusEvolution #GenomicSurveillanceย  ๐Ÿ“„ https://doi.org/10.3390/v18070724 ๐Ÿ‘ค EVBC member: Cesare Gruber

doi.orgConvMut: Exploration of Viral Convergent Mutations Along Phylogenies | MDPIConvergent evolution in protein antigens is common across pathogens, including SARS-CoV-2; the most likely reason is the need to evade the selective pressure exerted by previous infection- or vaccine-elicited immunity.

An adapted AlphaFold2-Multimer workflow predicts both pre- and postfusion conformations of class I virus fusion proteins, supporting structure-based epitope mapping and vaccine design ๐Ÿงฌ๐Ÿค– #AlphaFold #VaccineDesign ๐Ÿ“„ https://doi.org/10.1371/journal.pone.0351662 ๐Ÿ‘ค EVBC: Clara Schoeder, Jens Meiler

doi.orgPrediction of pre- and postfusion conformations of class I fusion proteins with AlphaFold2Viruses such as coronaviruses or filoviruses use their surface glycoproteins (GPs) to attach to the host cell, triggering the fusion of the viral membrane with the endosome membrane. Epitopes on the viral GP are major targets for antibody-mediated recognition and neutralization. During the fusion process, the GP undergoes conformational changes triggered by fluctuations in environmental pH. Structural states are typically classified into three distinct conformations: prefusion, intermediate, and postfusion. These conformations serve as essential templates for prediction of conformational epitopes and structure-based vaccine design. Despite their importance, many viral GP structures remain absent from the Protein Data Bank (PDB). Fortunately, recent breakthroughs in computational structure prediction have greatly enhanced the accuracy and accessibility of protein modeling. In this study, we utilized AlphaFold2-Multimer (AF2-M), version 2.3, to predict various GP structural conformations and observed that the overall frequency of predictions in the postfusion conformation is low. Therefore, we hypothesized that adapting the AF2-M protocol is necessary to enrich for specific conformations, thereby enabling the prediction of both pre- and postfusion conformations. AF2-M requires only the input sequence and internally generates multiple sequence alignments (MSAs) and optional templates before applying its pretrained model weights. We tested the use of template data to enrich pre- or postfusion conformations and demonstrated that our approach significantly increases the prediction frequency of class I fusion protein structures in both conformations, with the template dataset playing a crucial role in guiding modeling towards the intended state. Furthermore, we showed that the lack of correlation between pLDDT and TM-scores suggests that low pLDDT values may obscure the presence of valid alternative conformations.

A new study presents VirBench and gget virus, a deterministic tool for reproducible virus sequence retrieval. It raised AI-agent accuracy to โ‰ฅ90% and reduced representative data transfer by 98% ๐Ÿงฌ๐Ÿค– #VirusGenomics #AI ๐Ÿ“„ https://doi.org/10.48550/arXiv.2606.06749 ๐Ÿ‘ค EVBC: Bernhard Renard, Laura Luebbert

doi.orgDeterministic access to global viral sequence data enables robust agentic scientific discoveryPublic viral genome resources such as the National Center for Biotechnology Information (NCBI) Virus database are central to outbreak response, evolutionary analysis, vaccine design, and genomic surveillance. Yet many high-value retrieval workflows remain optimized for interactive use rather than deterministic, reproducible programmatic interfaces. This creates a challenge for Large Language Model (LLM)-based scientific agents, where errors in metadata interpretation, filtering logic, or retrieval can propagate into incorrect datasets. To evaluate agentic viral data retrieval, we built VirBench, a manually curated benchmark of 120 queries spanning diverse pathogens, taxonomic levels, and metadata filters. When autonomous AI systems, including Biomni, Claude, GPT, and Edison Analysis, were tasked with these queries without a dedicated retrieval layer, performance varied widely: mean accuracy ranged from 16.9% for Claude Sonnet 4 to 91.3% for GPT-5.5, with newer frontier models showing progress but residual errors remaining consequential. To address this, we built gget virus, a deterministic query framework that formalizes NCBI Virus-style filtering as a reproducible programmatic system. By staging retrieval, applying metadata constraints before sequence download, and retrieving structured GenBank records, gget virus reduces data transfer by more than 98% for high-volume queries while preserving exact-match semantics. Instructing autonomous AI systems to use gget virus increased accuracy to at least 90.0% across all evaluated systems and up to 99.7% for GPT-5.5, improved response stability to 0.92-1.00, reduced error magnitude, and generally decreased runtime and tool calls. Together, this work establishes deterministic data access as critical infrastructure for reliable agentic science and provides a reproducible retrieval layer for robust human- and AI-driven viral genomics workflows.

A scalable RB-TnSeq screen identifies 42 genes required for infection by 25 Klebsiella phages, revealing conserved and phage-specific requirements and informing phage host-range prediction and cocktail design. ๐Ÿฆ  ๐Ÿ“„ doi.org/10.1371/jour... ๐Ÿ‘ค EVBC member: Matthew B. Sullivan

doi.orgCross-family and phage-specific gene requirements for Klebsiella infection revealed by scalable RB-TnSeq genetic screensAuthor summary Bacteriophages, or phages, are viruses that infect bacteria and play central roles in shaping microbial communities across ecosystems. Despite their ecological importance, the bacterial...

European Virus Bioinformatics Center reposted

๐Ÿ“ขJoin us for the next ECR #Viromics Webinar "Understanding the viral composition and the dynamic phage-bacterial interplay in Idiopathic nephrotic syndrome" โ€๐ŸŽ™๏ธ Eman W. Abdelsalam, Sidra Medicine, Qatar ๐Ÿ—“๏ธ 12 Aug 2026, 4 PM CEST ๐Ÿ“ Zoom (register for login details) ๐Ÿ‘‰ evbc.uni-jena.de/events/ecr-v...

European Virus Bioinformatics Center reposted

Me, @emma-harding.bsky.social, @rtarlinton.bsky.social and @royalsociety.org are organising a meeting on endogenous viral elements! 8-9 Feb 2027, Birmingham UK. 2 whole days of EVEs! Many amazing researchers already agreed to speak. Invites: shorturl.at/jp9sh Provisional schedule: shorturl.at/8O5KV

royalsociety.orgEndogenous viral elements | Royal SocietyTheo Murphy meeting organised by Dr Katy Brown, Dr Emma Harding and Professor Rachael Tarlinton

Large-scale analysis of #LassaVirus sequences reveals lineage-specific biophysical features and delivers comprehensive #glycoprotein structure catalogue, supporting vaccine and therapeutic development๐Ÿฆ ๐Ÿงฌ ๐Ÿ“„ https://doi.org/10.1038/s44298-026-00196-3 ๐Ÿ‘ค EVBC: Knut Reinert, Clara Schoeder, Denise Kรผhnert

doi.orgSequence to structure insights into Lassa virus population-level biophysical properties and glycoprotein structure catalogue - npj Virusesnpj Viruses - Sequence to structure insights into Lassa virus population-level biophysical properties and glycoprotein structure catalogue

Structure-based prediction of #phage proteins (Phage Homomer Level Estimate and Generation Method PHLEGM) uses #AlphaFold Multimer and interface scoring to resolve thousands of virus protein complexes from sequence data๐Ÿงฌ๐Ÿ’ป #StructuralBiology ๐Ÿ“„ doi.org/10.64898/202... ๐Ÿ‘คEVBC: Robert Edwards, Bas Dutilh

doi.orgComputational prediction resolves thousands of homooligomeric phage protein structuresBacteriophages (phages) play essential roles in microbial systems, yet most phage proteins remain poorly characterised. Protein tertiary and quaternary structure information contributes valuable infor...

A new open-access catalogue brings together all known human-infective RNA viruses, providing a valuable resource for virology, surveillance, and pandemic preparedness. ๐Ÿฆ ๐Ÿ“Š #Virology #InfectiousDiseases #OpenData ๐Ÿ“„ https://doi.org/10.1038/s41597-026-07281-5 ๐Ÿ‘ค EVBC member: Liam Brierley

doi.orgA complete catalogue of human-infective RNA viruses - Scientific DataScientific Data - A complete catalogue of human-infective RNA viruses

European Virus Bioinformatics Center reposted

๐Ÿ“ข Join us for the next Viruses in silico webinar lecture! ๐ŸŽ™๏ธ "The ICTV at Sixty Years: Classifying the Worldwide Virosphere" ๐Ÿ‘จโ€๐Ÿ”ฌ Elliot J. Lefkowitz (University of Alabama at Birmingham, US) ๐Ÿ—“๏ธ 25 June 2026 ๐Ÿ•‘ 4 PM CEST ๐Ÿ“ Zoom - Register to receive the login details ๐Ÿ‘‰ evbc.uni-jena.de/events/virus...

European Virus Bioinformatics Center reposted

A recent The New York Times article on treatment advances for the Bundibugyo #Ebola outbreak follows GVN's June 10 media briefing featuring Prof. Jean-Jacques Muyembe, Ebola research expert and Director of INRB. Read the article: https://ow.ly/rlTi50ZblRe #GlobalVirusNetwork #GVN #Ebola

ow.lyScientists Race to Test Treatments as Ebola Outbreak WidensTrials are beginning on several drugs that have shown promise in preliminary studies against the virus that is causing the current outbreak.

Congratulations to the #ViBioM2026 award winners! ๐Ÿฅ‡Best ECR Talk: Dr. Emma Harding, University of Oxford ๐Ÿ‡ฌ๐Ÿ‡ง ๐Ÿฅ‡Best Poster: Aistฤ—ลฝidonytฤ—, Vilnius University ๐Ÿ‡ฑ๐Ÿ‡น Sponsored by Viruses (MDPI)๐Ÿ™ Thank you to all the speakers and poster presenters!

Back on track with Day 3 of #ViBioM2026! After two engaging days of talks, posters, discussions, quizzes, and challenges, we are looking forward to more talks and discussions on #virus #bioinformatics. Great to see such active exchange throughout the meeting ๐Ÿซถ #ScientificExchange

๐ŸŒŸ Day 1 of #ViBioM2026 at Vilnius University ๐Ÿ›๏ธ with a warm welcome by Manja, Gytis, and Ingrida โ€“ we already feel at home! Excited to start a full programme of talks, posters, and discussions on computational approaches in #virology. #viralgenomics #datascience #virusevolution

Nuoลกirdลพiai sveiki atvykฤ™! #ViBioM2026 is underway in Vilnius!๐ŸŽ‰๐Ÿ‡ฑ๐Ÿ‡น It's great to see participants arriving and connecting at todayโ€™s welcome get-together ๐Ÿค๐Ÿบย  Excited for the days ahead, filled with talks, posters, and discussions across #virology and #bioinformatics ๐Ÿงฌ๐Ÿ’ปย  #researchcommunity