The International Virus Bioinformatics Meeting 2024 was held in Leuven, Belgium, from 28–30 May 2024, attracting approximately 160 participants worldwide. ViBioM 2024 is jointly organized by the European Virus Bioinformatics Center, the KU Leuven, and the Université Libre de Bruxelles.
Organizing Committee
Simon Dellicour
Franziska Hufsky
Liana Kafetzopoulou
Philippe Lemey
Manja Marz
Jelle Matthijnssens
The three-day meeting fostered highly interactive exchanges among participants. It served as a key platform for gaining valuable insights into the current state of virus bioinformatics research while engaging with both established and emerging scientists. The event comprised seven invited talks, 20 contributed talks, and 74 poster presentations, organized into eight sessions over the course of three days. The topics covered a broad range of areas, including viral evolutionary history, human virus evolution, viral protein structure, machine learning, viral proteomics, virus-host interactions, surveillance, epidemiology, and viral sequence analysis.
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 globe.
Invited Speakers
Yves Briers
Ghent University
Nathan Grubaugh
Yale School of Public Health
Lia van der Hoek
University of Amsterdam
Mart Krupovic
Institut Pasteur
Vera van Noort
KU Leuven / Leiden University
Houriiyah Tegally
Stellenbosch University
Featured talk invited by the VIROINF project:
Alexander Gorbalenya
Leiden University
Awardees
PhD Travel Award:
Best Scientific Poster Award:
Best ECR Talk Award:
Special Issues
Simultaneously to the meeting, we have published a special issue on Virus Bioinformatics in Viruses.
Program Schedule
Find the list of all abstracts here.
Tuesday, 28. May 2024
| 08:30 | Registration desk opens |
| 09:00 – 09:30 | Welcome and opening remarks Manja Marz (EVBC Director) Jelle Matthijnssens, Philippe Lemey, Simon Dellicour (Local Organizers) |
| 09:30 – 10:00 |
Opening talk invited by VIROINF 1984 Alexander Gorbalenya | Leiden University, Netherlands Chair: Manja Marz |
| 10:00 – 10:30 | Coffee break |
| Session 1 | Viral Evolutionary History Chair: Dmitrij Frishman |
| 10:30 – 11:00 | Keynote talk Disentangling the evolutionary history of varidnaviruses Mart Krupovic | Institut Pasteur, France Chair: Manja Marz |
| 11:00 – 11:20 |
Phylogenetic Evidence for Viral Eukaryogenesis Sangita Karki | Virginia Tech, Blacksburg, United States |
| 11:20 – 11:40 |
Proir consideratoins for tests of temporal signal in ancient pathogen genomics Sebastian Duchene | Institut Pasteur, Paris, France |
| 11:40 – 12:00 |
Exploration of the Updated Diversity of Helicase Superfamilies 1 and 2 Reveals New Families and Presence of Multiple Transfer Events Between Viruses and Cells Anamarija Butkovic | Institut Pasteur, Paris, France |
| 12:00 – 13:30 | Lunch break |
| 13:30 – 14:00 | Poster Pitches A |
| 14:00 – 15:30 | Poster Session A |
| 15:30 – 16:00 | Coffee break |
| Session 2 | Evolution of Human Viruses Chair: Lara Fuhrmann, Philippe Lemey |
| 16:00–16:30 |
Keynote talk Anellovirus in humans, do we live happily ever after? Lia van der Hoek | University of Amsterdam, Netherlands Chair: Philippe Lemey |
| 16:30 – 16:50 |
The prevalence of back-and-forth substitutions in the evolutionary landscape of human viruses Florian Poulain | University of Liege, Liège, Belgium |
| 16:50 – 17:10 |
Characterization of HIV-1 Genome in A Long-Term Experimental Evolution Study Ali Movasati | University of Zurich / University Hospital Zurich, Zurich, Switzerland |
Wednesday, 29. May 2024
| 09:30 – 10:00 |
Keynote talk Unleashing molecular lego inspired by bacteriophage evolution Yves Briers | Ghent University, Belgium Chair: Jelle Matthijnssens |
| Session 3 | Viral Protein Structure Chair: Philippe Le Mercier |
| 10:00 – 10:20 |
Phold: Using Protein Structural Homology & Protein Language Models to Enhance Phage Genome Annotation George Bouras | The University of Adelaide, Adelaide, Australia |
| 10:20 – 10:40 |
Mapping glycoprotein structure reveals defining events in the evolution of the Flaviviridae Jonathon Mifsud | University of Sydney, Sydney, Australia |
| 10:40 – 11:00 |
Characterisation and monitoring of SARS-CoV-2 and future emergent viruses using protein language models Kieran Lamb | MRC-University of Glasgow Centre for Virus Research, Glasgow, Scotland |
| 11:00 – 11:30 | Coffee break |
| Session 4 | Machine Learning for Viral Proteomics Chair: Anne Kupczok |
| 11:30 – 11:50 |
Adapting broad protein language models to viruses Spyros Lytras | University of Tokyo, Tokyo, Japan |
| 11:50 – 12:10 |
Explaining Influenza A Neuraminidase Classification Results from a Biological Perspective using Interpretable Machine Learning Models Lynn V. Reuss | University of Applied Sciences Mittweida, Mittweida, Germany |
| 12:10 – 12:30 | Improved prediction of protein-protein interactions using a next sentence cross-encoder Dan Liu | University of Glasgow, Glasgow, United Kingdom |
| 12:30 – 14:00 | Lunch break |
| 14:00 – 14:30 | Poster Pitches B |
| 14:30 – 16:00 | Poster Session B |
| 16:00 – 16:30 | Coffee break |
| Session 5 | Virus-host-interaction Chair: Janina Rahlff |
| 16:30–17:00 |
Keynote talk A system view on phage-host interactions using transcriptomics and acetyl-proteomics Vera Van Noort | KU Leuven, Netherlands Chair: Jelle Matthijnssens |
| 17:00 – 17:20 |
Decoding the blueprint of filovirus entry through large-scale binding assays and machine learning Gorka Lasso | Albert Einstein College of Medicine, New York, United States |
| 17:20 – 17:40 |
The Intriguing World of Unknowns: exploration of Polycipiviridae genomes, Phylogenetics and Host Specificity Ingrida Olendraite | University of Cambridge, Cambridge, United Kingdom |
| 19:00 | Conference Dinner Restaurant Mykene, Muntstraat 44, 3000 Leuven, Belgium |
Thursday, 30. May 2024
| Session 6 | Surveillance / Epidemiology I Chair: Sebastian Lequime |
| 09:30 – 10:00 |
Keynote talk Towards a global virus genomic surveillance system Nathan Grubaugh | Yale School of Public Health, United States Chair: Philippe Lemey |
| 10:00 – 10:20 |
Shotgun metagenomics on air: Longitudinal surveillance of viruses in a daycare center Mustafa Karatas | KU Leuven, Leuven, Belgium |
| 10:20 – 10:40 |
Molecular characteristics of a localized influenza A(H1N1) pdm09 outbreak in South Africa, 2020 Dikeledi Kekana | National Institute for Communicable Diseases, Johannesburg, South Africa |
| 10:40 – 11:10 | Coffee break |
| Session 7 | Viral sequence analysis Chair: Daniel Todt |
| 11:10 – 11:30 |
Representative full-genome alignments of viral clades – a semi-automated approach incorporating amino acids, nucleotides & RNA secondary structures Sandra Triebel | Friedrich Schiller University Jena, Jena, Germany |
| 11:30 – 11:50 |
detectEVE: Illuminating the hidden viral footprint in genomic data Nadja Brait | University of Groningen, Groningen, Netherlands |
| 11:50 – 12:10 |
varVAMP: automated pan-specific primer design for tiled full genome sequencing of highly diverse viral pathogens Jonas Fuchs | Institut für Virologie, Universtitätsklinikum Freiburg, Freiburg, Deutschland |
| 12:10 – 13:50 | Lunch break |
| Session 8 | Surveillance / Epidemiology II Chair: Joana Abrantes |
| 13:50 – 14:20 |
Keynote talk CLIMADE: Pandemic Preparedness for Arboviruses in a time of Climate Change Houriiyah Tegally | Stellenbosch University, South Africa Chair: Simon Dellicour |
| 14:20 – 14:40 | Hendra virus in Australian bats show a diffuse spatio-temporal structure Claude Yinda Kwe | NIAID/NIH, Hamilton, USA |
| 14:40 – 15:00 |
Sequencing error inspires novel phylogenetic approaches to sequence data Chris Illingworth | MRC-University of Glasgow Centre for Virus Research, Glasgow,UK |
| 15:00 – 15:45 | Annual Meeting of the EVBC |
| 15:45 – 16:15 | Closing ceremony / awards |
Poster Sessions
Highlighted posters were be pitched in a snapshot presentation immediately before the poster session.
Some of the posters are shared by the authors. Please find them here.
Poster Session A
| A01 | Assessing distinctiveness profiling for predicting SARS-CoV-2 variant success A S M Rubayet Ul Alam | University of Glasgow, Glasgow, United Kingdom |
| A04 | A novel Illumina iSeq100-based next-generation sequencing (mNGS) pipeline for virus discovery, genomics and outbreak prevention/management Daniel Cadar | Bernhard Nocht Institute for Tropical Medicine, Hamburg, Germany |
| A05 | GUT VIROME IS ASSOCIATED WITH SUBSEQUENT CELIAC DISEASE IN TWO EUROPEAN PROSPECTIVE BIRTH COHORTS Katerina Chuda | Charles University, Second Faculty of Medicine, Prague, Czechia |
| A06 | Genome Detective dengue subtyping tool Sara Cleemput | Emweb, Herent, Belgium |
| A07 | Cameroonian onchocerciasis vectors (Diptera: Simuliidae) harbor a plethora of novel (RNA) viruses Lander De Coninck | KU Leuven, Leuven, Belgium |
| A08 | Virus-host interplay in polar sea ice Tatiana Demina | Helsinki University, Helsinki, Finland |
| A09 | Evolution of Crassvirales in the context of their hosts Mikhail Fofanov | Friedrich Schiller University Jena / Utrecht University, Jena, Germany |
| A10 | Phylogeographic history of SARS-CoV-2 variants in Spain Pilar Gallego-García | Universidade de Vigo, Vigo, Spain |
| A11 | Navigating sampling bias in discrete phylogeographic analysis: assessing the performance of an adjusted Bayes factor Fabiana Gambaro | ULB, Brussels, Belgium |
| A12 | Extrahepatic replication and genomics signatures of the hepatitis E virus in the kidney André Gömer | Ruhr University Bochum, Bochum, Germany |
| A13 | Epidemiology and global spread of emerging tick-borne Alongshan virus Saskia Janshoff | Ruhr University Bochum, Bochum, Germany |
| A14 | Surveillance of dengue and other arboviruses in mosquitoes from Dar es Salaam, Tanzania Silvan Hälg | Swiss TPH, Allschwil, Switzerland |
| A15 | Unravelling the Virome from Different Anatomical Sites in Psoriasis Patients Dominika Kadlečková | Charles University, Faculty of Science, Prague, Czechia |
| A16 | Kijin Kim | Simon Fraser University, Richmond, Canada |
| A17 | Viralgenie, a pipeline for viral metagenome sequencing data: applications in Lassa virus research Joon Klaps | KULeuven, Leuven, Belgium |
| A18 | Detecting recombination events in closely related viruses from sequence data Sarah Krautwurst | Friedrich Schiller University Jena, Jena, Germany |
| A19 | ViralZone enzymes: improved overview of the viral reaction landscape. Philippe Le Mercier | Swiss Institute of Bioinformatics, Geneva, Switzerland |
| A20 | Data and Resources of the International Committee on Taxonomy of Viruses: ICTV Elliot Lefkowitz | University of Alabama at Birmingham, Birmingham, Alabama, USA |
| A21 | Data and resources of the Bacterial and Viral Bioinformatics Resource Center (BV-BRC) Elliot Lefkowitz | University of Alabama at Birmingham, Birmingham, Alabama, USA |
| A22 | Unveiling Ribes virome: A Comprehensive Exploration Study Rebeka Ludviga | Latvian Biomedical Research and Study centre, Riga, Latvia |
| A23 | Sex and viruses: specific virome structure between males and females depending on mosquito species Côme MOREL | CIRAD / UMR ASTRE, Montferrier-sur-Lez, France |
| A24 | Diversity and evolution of the deltavirus-like agents in termites Jose Gabriel Nino Barreat | University of Oxford, Oxford, United Kingdom |
| A25 | Revealing dynamic genomic rearrangements in hepatitis E virus infection using Hyper-Eins Maximilian Klaus Nocke | Ruhr University Bochum, Bochum, Germany |
| A26 | Insights into the gut microbiota development in healthy Bangladeshi infants: exploring the gut virome during early life. Maria Ioanna Papadaki | KU Leuven, Leuven, Belgium |
| A27 | Phage hunting at the air-water boundary of the Central Arctic Janina Rahlff | Linnaeus University, Kalmar, Sweden |
| A28 | Virome analyses of metatranscriptome data using NeoRdRp Shoichi Sakaguchi | Osaka Medical and Pharmaceutical University, Takatsuki, JAPAN |
| A29 | Dissecting the gene expression dynamics during early HCMV infection Lygeri Sakellaridi | University of Regensburg, Würzburg, Germany |
| A30 | Determinants of Species-Specific Hepatitis E Virus Pathogenicity Leyla Sirkinti | Ruhr University/ Medical Virology, Bochum, Germany |
| A31 | Paint4IRAS. Development of biocidal paints against viruses and bacteria in healthcare settings. David Talavera Cortés | Universitat de València, Valencia, Spain |
| A32 | Exploration the virome of European mosquitoes Gabor Toth | Bernhard-Nocht Institute for Tropical Diseases, Hamburg, Germany |
| A33 | Phosphoproteomic analysis of Aedes aegypti Aag-2 cells infected with the arboviruses MAYV and CHIKV Anna Fernanda Vasconcellos | University of Brasilia, Brasília, Brazil |
| A34 | A deep learning pipeline for Bacteriophage detection Rajitha Yasas Wijesekara | University Medicine Greifswald, Greifswald, Germany |
| A35 | VAZyMolO-2 – How did you annotate your new viral genome without it ? Vincent WILDE | CNRS-UMR725 (AFMB), Marseille, France |
| A36 | Using protein language models to investigate the evolutionary processes leading to virus attenuation Francesca Young | MRC University of Glasgow Centre for Virus Research, Glasgow, UK |
| A37 | Mriyaviricetes: a new class of viruses related to Nucleocytoviricota Natalya Yutin | NCBI, Bethesda, USA |
| A38 | Are C-terminal anchor (CTA) endolysins a thing? Identification of possible CTA endolysins across sequences of uncultivated bacteriophages Nikita Zrelovs | Latvian Biomedical Research and Study Centre; University of Latvia, Riga, Latvia |
| A39 | Genomic monitoring to unravel the emergence and maintenance of arboviruses in the Netherlands Emmanuelle Münger | Erasmus MC Rotterdam, Netherlands |
Poster Session B
| B01 | The Virome of the Western Honey Bee in Europe Nikolas Basler | KU Leuven, Leuven, Belgium | |
| B02 | Identification of tandem repeats of an endogenous RdRp-like element in multiple species of butterfly and moth. Katy Brown | University of Cambridge, Cambridge, UK | |
| B03 | On the importance of assessing topological convergence in Bayesian phylogenetic inference Marius Brusselmans | KU Leuven, Leuven, Belgium | |
| B04 | Virus metagenomics reveals high diversity of novel newlaviruses in Canadian seals Marta Canuti | University of Copenhagen, Copenhagen, Denmark | |
| B05 | Phage genome architecture and GC content: Structural genes and where to find them Ritam Das | Aero-Aquatic Virus Research Group, Friedrich Schiller University Jena, Jena, Germany | |
| B06 | BLMPred: predicting linear B-cell epitopes using pre-trained protein language models and machine learning Barnali Das | Technical University of Munich, Munich, Germany | |
| B07 | Disentangling viral strains using long reads Roland Faure | Université Libre de Bruxelles, Brussels, Belgium | |
| B08 | Evaluation of Different Extraction Techniques of Skin Samples for Virome Analysis Lisa Faye | KU LEUVEN, Leuven, Belgium | |
| B09 | VILOCA: Local haplotype reconstruction and mutation calling for short- and long-read viral sequencing data Lara Fuhrmann | ETH Zurich, Basel, Switzerland | |
| B10 | Exploring the human virome in chronic liver disease with integrated viral and bacterial metagenomics data Emilio Rafael Garcia Rios | TUM, Freising, Germany | |
| B11 | Assessing the genetic stability of phage therapeutic products through deep sequencing Nathalie Goeders | Sciensano, Brussels, Belgium | |
| B12 | Coupling homology search and network analysis for OTU clustering in eukaryotic viromes Serafin Gutierrez | CIRAD, Montpellier, France | |
| B13 | Bioinformatic analysis of clinical samples from an HEV-infected pregnant woman using metagenomics Marta Ibañez-Lligoña | Vall d’Hebron Institute of Research (VHIR), Barcelona, Spain | |
| B14 | Viral metagenomic workflow for identification of viruses from bats Camille Johnston | Statens Serum Institut, Copenhagen, Denmark | |
| B15 | Detection of RNA viruses in Dutch natural plant ecosystems Dimitris Karapliafis | Wageningen University & Research, Wageningen, Netherlands | |
| B16 | Phage-Antibiotic Synergy: definition, evaluation & prediction Eliška Kučerová | Masaryk University, Brno, Czech Republic | |
| B17 | Catching them all: Assessing the diversity and evolution of Iflaviridae genomes found in publicly available Lepidoptera sequencing data Anne Kupczok | Wageningen University, Wageningen, Netherlands | |
| B18 | RNAswarm: Differential Analysis of RNA-RNA Interactions in Influenza A Virus Gabriel Lencioni Lovate | Friedrich Schiller University Jena, Jena, Germany | |
| B19 | Spread.gl: Visualising Pathogen Dispersal in a High-performance Browser Application Yimin Li | Rega Institute, Leuven, Belgium | |
| B20 | Improved prediction of protein-protein interactions using a next sentence cross-encoder Dan Liu | University of Glasgow, Glasgow, United Kingdom | |
| B22 | Ancient viral discoveries through ancient metagenomic data Luca Nishimura | The University of Tokyo, Minato-ku, Japan | |
| B23 | The Intriguing World of Unknowns: exploration of Polycipiviridae genomes, Phylogenetics and Host Specificity Ingrida Olendraite | University of Cambridge, Cambridge, United Kingdom | |
| B24 | Impact of genetic reassortment on the structure of RNA genomic segments of Influenza A viruses Rithu Paul Stansilaus | University of Strasbourg, Strasbourg, France | |
| B25 | Transmission-mediated adaptation of virulence in Deformed Wing Virus Harshit Kumar Prajapati | Freie Universität Berlin, Berlin, Germany | |
| B26 | Genomic Echoes: Exploring Challenges and Opportunities in Identifying Endogenous Viral Elements Muriel Ritsch | Friedrich Schiller University Jena, Jena, Germany, Jena, Germany | |
| B27 | Exploring the in-silico molecular docking method to study the interactions of novel entry inhibitors against multiple HIV subtypes. ARADHANA SINGH | SOUTH ASIAN UNIVERSITY, NEW DELHI, INDIA | |
| B29 | Assessment of COVID-19 contact tracing network accuracy via phylogenetic analysis of community-level SARS-CoV-2 genomic data Jonathan Thibaut | Catholic University of Leuven (KU Leuven), Leuven, Belgium | |
| B30 | Control of human anelloviruses by cytosine to uracil genome editing Anne Timmerman | Amsterdam UMC, Amserdam, Netherlands | |
| B31 | Dissecting the unknown specificity of cell wall-binding domains of phage endolysins Roberto Vázquez | Ghent University, Ghent, Belgium | |
| B32 | From water to wild plants: exploring plant virus diversity of various sample types through high-throughput sequencing data analysis. Lana Vogrinec | National Institute of Biology, Ljubljana, Slovenia | |
| B33 | Viral community diversity decreases from the bulk soil to the rhizosphere Lingyi Wu | Utrecht University, Utrecht, Netherlands | |
| B34 | Dissect antiviral immunity in pluripotent stem cells via single-cell transcriptomics Qing Yang | Fred Hutchinson Cancer Center, Seattle, United States | |
| B35 | Identification of a tomato brown rugose fruit virus mutant isolate overcoming virus-specific resistance in new resistant tomato cultivar Zafeiro Zisi | Laboratory of Viral Metagenomics, KU Leuven & Scientia Terrae, Leuven, Belgium | |
| B36 | Comparative Evaluation of Bioinformatic Pipelines for Full-Length Viral Genome Assembly Levente Zsichla | Eötvös Loránd University, Budapest, Hungary | |
| B37 | Parallel evolution of Drosophila C virus independent of host RNAi status Oscar Morales Lezcano | Radboudumc, Nijmegen, Netherlands | |
| B38 | Fragmentation of AlphaFold structures for improved interaction prediction Stefaan Verwimp | KU Leuven, Leuven, Belgium | |
| B39 | Comparison of R9 and novel R10 Nanopore flow cells for mixed multiplexed viral amplicon sequencing David Nieuwenhuijse | Erasmus MC Rotterdam, Netherlands |
Sponsors
We would like to thank our sponsors for supporting the International Virus Bioinformatics Meeting 2024!
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