The International Virus Bioinformatics Meeting 2025 was held in Lisboa, Portugal, from 13–15 May 2025, attracting approximately 150 participants from over 34 countries worldwide. ViBioM 2025 was jointly organized by the European Virus Bioinformatics Center, the Instituto de Higiene e Medicina Tropical, and the Universidade Nova de Lisboa.
ViBioM 2025 served as a platform for the highly interactive exchange among participants and for gaining valuable insights into the current state of virus bioinformatics research by engaging with an extensive network of experts in virology and bioinformatics of both established and emerging scientists. The event comprised six invited talks, 18 contributed talks, and 78 poster presentations across eight sessions over the course of three days. Topics covered a broad range of areas, including virus evolution and ancient viruses, virus adaption, virus detection and classification, virus protein interactions, virus surveillance, bacteriophages, and SARS-CoV-2. ViBioM has become synonymous with cross-disciplinary scientific exchange and dialogue, attracting some of the most influential researchers and young scholars in virology and bioinformatics from around the world.
Organizing Committee
Ana B. Abecasis
Inês Martins Alves
Joana Abrantes
Paula Istvan
Manja Marz
Sofia Gonçalves Seabra
Invited Speakers
Marie Agnes Petit
Arvind Varsani
Denise Kühnert
Richard Neher
Maria Joao Amorim
Pieter Libin
Awardees
Best Scientific Poster Award: Kieran Lamb
Best ECR Talk Award: João Dourado
Program Schedule
Tuesday – 13 May 2025
| 09:00–09:30 | Registration — All sessions will take place at Aula Magna room – IHMT-NOVA |
| 09:30–10:00 | Welcome and Opening Remarks — Miguel Viveiros and Manja Marz |
| 10:00–10:30 | Keynote Talk: Making Sense of Lipidomic and Metabolomic Reprogramming in Influenza A Infected Host Cells Maria João Amorim, Medical School, Universidade Católica Portuguesa, Portugal |
| 10:30–11:00 | Coffee Break |
| Session 1: Ancient Viruses — Chair: Tatiana Demina | |
| 11:00–11:20 | An Orbi-Like Virus in Diverse Parasitic Nematodes with Circulating and Ancient Endogenous Forms Katy Brown, University of Cambridge, UK |
| 11:20–11:40 | Decoding the Paleovirology of Retroviruses: Exploring Proviral Evolution and Invasion Patterns Across Mammalian Genomes Emma Harding, University of Oxford, UK |
| 11:40–12:00 | Accurate Reconstruction of Persistent Human Viral Sequences Maria J. P. Sousa, University of Aveiro, Portugal |
| 12:00–13:30 | Lunch Break |
| 13:30–14:00 | Poster Pitches A — Aula Magna room–IHMT-NOVA, Chair: Victor Pimentel |
| 14:00–15:30 | Poster Session A — Lobby 2nd Floor–IHMT-NOVA |
| 15:30–16:00 | Coffee Break |
| Session 2: Viral Adaptation — Chair: Joana Abrantes | |
| 16:00–16:30 | Keynote Talk: Recombination Reassortment and Accessories the Dynamic Lifestyle of Small DNA Viruses Arvind Varsani, Arizona State University, USA |
| 16:30–16:50 | Granger-Causality Analysis Reveals Antiviral Potential of Defective Viral Genomes from Time Series Data Mia Le, University of Hamburg, Germany |
Wednesday – 14 May 2025
| 09:15–09:45 | Announcements and Group Photo |
| Session 3: Surveillance — Chair: Bas Oude Munnink | |
| 09:45–10:15 | Keynote Talk: Optimising Epidemic Mitigation Policies with Reinforcement Learning Pieter Libin, VUB Artificial Intelligence Lab, Belgium |
| 10:15–10:35 | ISG Profiler: A High-Throughput Quantification Tool for Interferon-Stimulated Genes to Enhance Viral Surveillance Luca Nishimura, University of Tokyo, Japan |
| 10:35–10:55 | VIRUS-MVP: A Framework for Comprehensive Surveillance of Viral Mutations and Their Functional Impacts Zohaib Anwar, Simon Fraser University, Canada |
| 10:55–11:30 | Coffee Break |
| Session 4: Virus Detection and Classification — Chair: Spyros Lytras | |
| 11:30–11:50 | INSaFLU-TELEVIR+: An Open Web-Based Bioinformatics Platform for Metagenomic Pathogen Detection Joao Santos, INSA, Lisbon, Portugal |
| 11:50–12:10 | Virus Genome Reconstruction for the Integrated Genomic Surveillance in Germany Using Nextflow Thomas Krannich, Robert Koch Institute, Berlin, Germany |
| 12:10–12:30 | Unveiling the global urban virome: insights from wastewater metagenomics Nathalie Worp, Erasmus MC, Rotterdam, Netherlands |
| 12:30–14:00 | Lunch Break |
| 14:00–14:30 | Poster Pitch B — Aula Magna room–IHMT-NOVA, Chair: Joana Abrantes |
| 14:30–16:00 | Poster Session B — Lobby 2nd Floor–IHMT-NOVA |
| 16:00–16:30 | Coffee Break |
| Session 5: Evolution of Viruses — Chair: Ingrida Olendraite | 16:30–16:50 | The Evolution of Giant RNA Genomes in Nidoviruses Chris Lauber, TWINCORE, Hannover, Germany |
| 16:50–17:10 | What’s More? Transcriptome Mining Reveals Diversity and Evolution of Iflaviruses in Lepidoptera Anne Kupczok, Wageningen University, Netherlands |
| 17:10–17:40 | Keynote Talk: Unraveling the Evolution and Transmission of Infectious Pathogens Through Integrating Phylogenomics and Machine Learning Denise Kühnert, Robert Koch Institute, Germany |
| 20:00 | Conference Dinner at Cantina LX |
Thursday – 15 May 2025
| 09:15–09:30 | Announcements |
| Session 6: Phages Chair: Ricardo Parreira | |
| 09:30–10:00 | Keynote Talk: What Can We Say Reliably About Intestinal Viromes Marie-Agnès Petit, INRAE, France |
| 10:00–10:20 | Evolutionary Building Blocks of Phage Proteome Shed Light on Phage Protein Recombination and Adaptation Emerging at Subdomain Level Bogna Smug, Jagiellonian University, Kraków, Poland |
| 10:20–10:40 | Insights and Caution from a CRISPR Spacer Analysis on a Global Scale Uri Neri, Joint Genome Institute, Berkeley, United States |
| 10:40–11:15 | Coffee Break |
| Session 7: Viral Proteins in Interaction Chair: Shoichi Sakaguchi | 11:15–11:35 | Capsid Renovations in Harsh Environments: Evolving a Stable Home for Your Genome Varada Khot, Friedrich Schiller University, Jena, Germany |
| 11:35–11:55 | Subgenomic Flaviviral RNAs and Human Proteins: In Silico Exploration of Anti-Host Defense Mechanisms Riccardo Delli Ponti, Italian Institute of Technology, Genoa, Italy |
| 11:55–12:15 | A Protein Language Model for Predicting Viral Antigenic Maps and Exploring Their Evolution Shusuke Kawakubo, The Institute of Medical Science, The University of Tokyo, Japan |
| 12:15–13:45 | Lunch Break |
| 13:45–14:30 | EVBC Meeting |
| Session 8: SARS-CoV-2 Chair: Vitor Borges | 14:30–14:50 | SARS-CoV-2 Evolution on a Dynamic Immune Landscape Sofia Paraskevopoulou, Robert Koch Institute, Berlin, Germany |
| 14:50–15:10 | CoVFit: A Protein Language Model for Exploring the SARS-CoV-2 Fitness Landscape Jumpei Ito, University of Tokyo, Japan |
| 15:10–15:15 | Final Voting Break |
| 15:15–15:45 | Keynote Talk: Mutation Purifying Selection and Adaptive Evolution of SARS-CoV-2 Richard Neher, University of Basel, Switzerland |
| 15:45–16:15 | Closing Ceremony & Prize Giving |
Poster Sessions
Highlighted posters were be pitched in a snapshot presentation immediately before the poster session.
Poster Session A
| A01 | Prediction of potential virus variation and antigenicity from a single sequence using a protein language model A S M Rubayet Ul Alam | MRC University of Glasgow Centre for Virus Research, Glasgow, UK |
| A02 | Vclust: accurate alignment and clustering of viral genomes at ultra scale Andrzej Zielezinski | Adam Mickiewicz University, Poznan, Poland |
| A03 | Validation of nanopore sequencing based test for untargeted plant virus detection using multiple process controls Anja Pecman | National Institute of Biology, Ljubljana, Slovenia |
| A04 | Utilizing whole genome sequencing data to unravel variations across rabies virus clades and improving diagnosis Ankeet Kumar | Indian Institute of Science, Bengaluru, India |
| A05 | The Virome of Fecal Microbiota Transplantation Donors and Recipients Büsra Külekci | University of Vienna, Vienna, Austria |
| A06 | Phylogenetic insights into the first Usutu virus outbreak in Denmark, 2024 Camille Johnston | Statens Serum Institut, Copenhagen, Denmark |
| A07 | Genomic insights into the global emergence of the phytopathogenic Maize yellow mosaic virus Damien Richard | French National Research Institute for Sustainable Development (IRD), Montpellier, France |
| A08 | Putative novel betaherpesvirus sequences identified in English shrews using whole-genome sequencing Dan Maskell | Animal and Plant Health Agency, Weybridge, UK |
| A09 | Applications of targeted metagenomic approaches for viral genomic surveillance and clinical metagenomics at the Portuguese National Institute of Health Daniel Sobral | Instituto Nacional de Saude Dr. Ricardo Jorge, Lisboa, Portugal |
| A10 | Goat Farming: Exploring the Virome at the Human-Animal Interface David Nieuwenhuijse | Erasmus MC, Rotterdam, Netherlands |
| A11 | Genome reconstruction for the integrated genomic surveillance of seasonal influenza in Germany Dimitri Ternovoj | Robert Koch Institute, Berlin, Germany |
| A12 | RdRpCATCH: A unified framework for RNA virus discovery based on RdRp profile databases Dimitris Karapliafis | Wageningen University & Research, Wageningen, Netherlands |
| A13 | Distribution of Giant Viruses and Mobile Genetic Elements in wastewater treatment plants Dominik Lücking | University of Vienna, CeMESS, Vienna, Austria |
| A14 | Phosphate amendment drives bloom of RNA viruses after soil wet-up Ella Tali Sieradzki | Aarhus University, Flakkebjerg, Denmark |
| A15 | New Website Features of the International Committee on Taxonomy of Viruses Elliot Lefkowitz | University of Alabama at Birmingham, Birmingham, USA |
| A16 | New Features of the Bacterial and Viral Bioinformatics Resource Center Elliot Lefkowitz | University of Alabama at Birmingham, Birmingham, USA |
| A17 | Find the Species: An ICTV Search Tool for Virus Taxon Names Elliot Lefkowitz | University of Alabama at Birmingham, Birmingham, USA |
| A18 | Deep learning methods for the clustering of viral sequences Emma Soufir | CIRAD/INSERM, Montpellier, France |
| A19 | Too variable? Evidence and potential causes for incongruent chuvirus genome organisations Emre Mert Asar | Vilnius University, Vilnius, Lithuania |
| A20 | Structure and diversity of the viral community is influenced by land use and mosquito species of Yucatan Mexico Erika Nayelli Hernández Villegas | UNAM, Mexico City, Mexico |
| A21 | Danish swine exports and the dissemination of swine influenza in Europe Esben B. Thuesen | Statens Serum Institut & University of Copenhagen, Copenhagen, Denmark |
| A22 | Inside the Engine Room of Austria’s Wastewater Surveillance Program Fabian Amman | Medical University Vienna, Vienna, Austria |
| A23 | Molecular Epidemiology of the Rabies Virus in Switzerland: From Outbreak to Eradication Farzane Shams | University of Bern, Bern, Switzerland |
| A24 | A Fast and Cost-Effective dsRNA Isolation Method for Viral Detection and Characterization Fernando Cardoso | IHMT – NOVA University of Lisbon, Lisboa, Portugal |
| A25 | Application of an Optimized dsRNA Isolation and DOP-RT-PCR Workflow for Broad Viral Detection in Yeast Model Fernando Cardoso | IHMT – NOVA University of Lisbon, Lisboa, Portugal |
| A26 | SnakeVir: A Snakemake Workflow for Viral Metagenomics Florian Charriat | Cirad, Montpellier, France |
| A27 | Investigating the complex evolutionary dynamics leading to viral attenuation. Francesca Young | MRC University of Glasgow Centre for Virus Research, Glasgow, UK |
| A28 | Unveiling Prophage Diversity in Acinetobacter baumannii: Evolutionary Insights and Antibiotic Resistance Threats Gamaliel Lopez-Leal | Center for Research in Cell Dynamics, Cuernavaca, Mexico |
| A29 | A pandemic in mosquitoes? Gytis Dudas | Life Sciences Center, Vilnius University, Vilnius, Lithuania |
| A30 | Genomic analysis reveals the ongoing 2024 Rift Valley Fever virus outbreak in Rwanda is related to the same strain circulating in 2022 in Rwanda Hayley Cassidy | Erasmus University Medical Center, Rotterdam, Netherlands |
| A31 | Evolutionary dynamics of circulating Influenza A and B viruses in the city of Sao Paulo between 2023 and 2024 Igor Ribeiro | Instituto Butantan, Sao Paulo, Brazil |
| A32 | Molecular Dynamics and Epidemiology of Influenza A and B Viruses in Brazil: Implications for Global Surveillance and Control (2021–2023) Isabela Brcko | Butantan Institute, Sao Paulo, Brazil |
| A33 | Local maintenance and genomic diversity of lymphocytic choriomeningitis virus in natural populations of house mice in the Czech Republic over a 24-year period Ivana Jezkova | Institute of Vertebrate Biology, Czech Academy of Sciences, Brno, Czech Republic |
| A34 | Unraveling Dengue Serotype 3 Transmission in Brazil: Evidence for Multiple Introductions of the 3III_B.3.2 Lineage James Siqueira Pereira | Instituto Butantan USP, Sao Paulo, Brazil |
| A35 | Assessing the genetic stability of mumps virus preparations for animal oncolytic virotherapy through RNA-seq Jelena Ivancic Jelecki | University of Zagreb, Zagreb, Croatia |
| A36 | Prophage Diversity in the Transfeminine Neovagina Jorge Rojas-Vargas | University of Western Ontario, London, Canada |
| A37 | Implementation of a data analysis pipeline for the genetic characterization of non-seasonal influenza A WGS samples in the context of laboratory surveillance of viral outbreaks João Pereira | INSA Dr. Ricardo Jorge, Lisboa, Portugal |
| A38 | Predicting viral evolution and epistatic effects with protein language models Kieran Lamb | MRC-University of Glasgow Centre for Virus Research, Glasgow, UK |
Poster Session B
| B01 | Unveiling plant virus diversity in aquatic plants through sequencing-based approaches Lana Vogrinec | National Institute of Biology, Ljubljana, Slovenia |
| B02 | suvtk: making viral genome submission FAIRly easy Lander De Coninck | KU Leuven, Leuven, Belgium |
| B03 | Proposal – Ecosystem within (EcoWhite): Exploring the virome and other microbiome members in whiteflies Laura Patioo Medina | Wageningen University & Research, Wageningen, Netherlands |
| B04 | Sequencing, epidemiology and development of a novel real-time PCR during the ongoing monkeypox virus clade Ib outbreak in eastern Africa Leonard Schuele | Erasmus MC, Rotterdam, Netherlands |
| B05 | Host factors in hepatitis e virus infection and species barriers Leyla Sirkinti | Ruhr University Bochum, Bochum, Germany |
| B06 | PREDICTORix: A scalable phylogeny-aware approach for quantifying viral spillover risk Li Chuin Chong | TWINCORE / MHH / DKFZ, Hannover, Germany |
| B07 | Exploring Eukaryotic Viruses and Bacteriophages in COPD Exacerbations Lisa Faye | KU Leuven, Leuven, Belgium |
| B08 | Enhancing Phage Virulence Prediction: New Methodologies and Comparative Assessment Maria Fernanda Silva Vieira | University of Minho, Braga, Portugal |
| B09 | Unveiling Pathogens and Contaminants: Refining Metagenomics for Clinical Diagnostics Marta Ibañez-Lligoña | Vall d’Hebron Institute of Research (VHIR), Barcelona, Spain |
| B10 | Extreme GC3 Codon Bias in a Novel Brown Seaweed Virus Results in Pseudoambigrammatic Characteristics. Martijs Jonker | University of Amsterdam, Amsterdam, Netherlands |
| B11 | Applying sequence projection and k-means as novel approach for Orthohepevirinae genotyping and species assignment Maximilian Nocke | Ruhr University Bochum, Bochum, Germany |
| B12 | Prophage-Encoded Phage Defense Systems Could Limit the Efficacy of Phage Treatments in Cystic Fibrosis Patients Meeri Piispa | University of Helsinki, Helsinki, Finland |
| B13 | Portable viral genomic surveillance with an easy-to-use Nanopore field sequencing pipeline Mia Le | Bernhard-Nocht-Institute for Tropical Medicine, Hamburg, Germany |
| B14 | Insights into genomic characterization of swine Influenza A Virus in Swiss pig populations. Mike Mwanga | University of Bern, Bern, Switzerland |
| B15 | Unraveling the evolution of the ASP gene in HIV-1 through computational analysis Miu Naruki | Institute for Advanced Biosciences, Keio University, Tsuruoka city, Japan |
| B16 | Genomic and proteomic analyses of WP-7 – Bacillus licheniformis bacteriophage Monika Dębińska | University of Gdansk, Gdansk, Poland |
| B17 | A multi-omics approach for gene prioritization highlights potential regulatory genes during phage infection Nand Broeckaert | KU Leuven, Leuven, Belgium |
| B18 | Whole-genome sequencing as a method for phage product identification and quality assessment Nathalie Goeders | Sciensano, Brussels, Belgium |
| B19 | Automating tobamovirus contig identification with snakemake and machine learning Neža Pajek Arambašič | University of Ljubljana, Ljubljana, Slovenia |
| B20 | Bacteriophages in a coastal ocean during a full year cycle-Ecological drivers of bacterial mortality during marine phytoplankton blooms Xinyu Tang | Max Planck Institute for Marine Microbiology, Bremen, Germany |
| B21 | Extending viral protein annotation with structural modeling: AlphaFold3 sheds light on reoviral capsid structures Philippe Le Mercier | Swiss Institute of Bioinformatics, Geneva, Switzerland |
| B22 | Discovery of Mushuviridae phages interacting with health-related human gut bacteria Piotr Rozwalak | Friedrich Schiller University / Adam Mickiewicz University, Germany / Poland |
| B23 | Identifying the Causative Agents of Crumbly Fruit Disease in Red Raspberry Plants in Latvia. Rebeka Ludviga | Latvian Biomedical Research and Study Centre, Riga, Latvia |
| B24 | Identifying putative regions of selective pressure using protein language models Robert Strange | University of Glasgow, Glasgow, UK |
| B25 | Virome Contaminants Matter: Pleading for the adoption of sequence controls Ryan Cook | Quadram Institute Bioscience, Norwich, UK |
| B26 | Untangling the gene regulatory network controlling immune activation and inflammation upon viral infection Sara Becker | Fred Hutchinson Cancer Center, Seattle, USA |
| B27 | The road towards a decision support tool for HEV treatment failure and chronicity Saskia Janshoff | Ruhr University Bochum, Bochum, Germany |
| B28 | Influence of urbanization and seasonality in the eukaryotic virome of the mosquito vector Culex pipiens Serafin Gutierrez | CIRAD, Montpellier, France |
| B29 | Enhanced RdRp profile HMMs capture conserved minor motifs for sensitive virus detection Shoichi Sakaguchi | Osaka Medical and Pharmaceutical University, Takatsuki, Japan |
| B30 | Expanding the genomic diversity of human anelloviruses Spyros Lytras | The University of Tokyo, Tokyo, Japan |
| B31 | Uncovering phage receptor signatures: Type IV Pili variation and host range in Pseudomonas aeruginosa Stefaan Verwimp | KU Leuven, Leuven, Belgium |
| B32 | Comparative Analysis of Subgenomic RNA Profiles across SARS-CoV-2 lineages in Hong Kong Tao Zhang | The University of Hong Kong, Hong Kong, China |
| B33 | The effect of reindeer grazing on soil viral communities in northern peatlands Tatiana Demina | Helsinki University, Helsinki, Finland |
| B34 | Identifying Modulators of Cellular Responses by Heterogeneity-sequencing Teresa Rummel | University Regensburg, Regensburg, Germany |
| B35 | Global diversity of circularised bacteriophages in metagenomes Valentyn Bezshapkin | ETH, Zurich, Switzerland |
| B36 | A single-cell transcriptomics approach to compare coronavirus infection in human and camelid primary airway epithelial cells Vera Flück | University of Bern, Bern, Switzerland |
| B37 | Insights from VAZyMolO-2 into the Phylogenetic History of Nidovirales Exonucleases Vincent Wilde | AFMB Luminy Marseille, Marseille, France |
| B38 | Exploring the Biological Sequence Space: Integration of Machine Learning and Mathematical Modeling in Viral Analysis Vinicius Carius de Souza | Butantan Institute, Sao Paulo, Brazil |
| B39 | Exploring phage-mediated adaptation of Ruminococcus gnavus to the human gut Xena Dyball | Quadram Institute Bioscience, Norwich, UK |
| B40 | Systematic search of associations between asfarviruses and eukaryotes Natalya Yutin | National Library of Medicine, National Institutes of Health |