Marie Agnes Petit- Research Institute for Agriculture, Food and Environment- Paris
Arvind Varsani- Arizona State University, USA
Denise Kühnert- Robert Koch Institute
Ludwign- Wildau
Richard Neher- University of Basel,Switzerland
Maria Joao Amorim- Biomedical Research Centre (CBR) - Lisbon, Portugal
Pieter Libin- Artificial Intelligence Lab - Brussels, Belgium
Program Schedule
Monday Evening May 12. 2025
| 19:00 |
Welcome Reception & Networking Event Venue: LX Factory (Entrance) |
Tuesday – May 13. 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 – May 14. 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 – May 15. 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 will 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 |