Event Calendar » International Virus Bioinformatics Meeting 2023

The International Virus Bioinformatics Meeting 2023 was held in Valencia, Spain, from 24–26 May 2023, attracting approximately 180 participants worldwide. ViBioM 2023 was jointly organized by the European Virus Bioinformatics Center, the Institute of Agrochemistry and Food Technology (IATA-CSIC), and the University of Valencia.

Organizing Committee

As the first in-person event following the SARS-CoV-2 pandemic, the meeting facilitated highly interactive exchanges among attendees. It served as a pivotal gathering for gaining insights into the current status of virus bioinformatics research and engaging with leading researchers and emerging scientists. The event comprised eight invited talks, 19 contributed talks, and 74 poster presentations across eleven sessions spanning three days. Topics covered included machine learning, bacteriophages, virus discovery, virus classification, virus visualization, viral infection, viromics, molecular epidemiology, phylodynamic analysis, RNA viruses, viral sequence analysis, viral surveillance, and metagenomics.

ViBioM has become synonymous with scientific exchange and dialogue between different disciplines and attracts some of the most influential scientists and young academics in virology and bioinformatics from around the world.

Invited Speakers

Satellite Meeting

The conference was preceded by the RdRp Summit, the first international conference dedicated to improving interoperability in the fields of RNA virus discovery and characterization.


PhD Travel Award: Yasas Wijesekara
Best Scientific Poster Award: Muriel Ritsch, Jordi Sevilla
Best ECR Talk Award: Lara Fuhrmann

Special Issues and Conference Report

Simultaneously to the meeting, we have published a special issue on Virus Bioinformatics in Viruses, including a conference report summing up the meeting.

Program Schedule

Find the list of all abstracts here.

Wednesday, May 24

09:00 — 09:30 Welcome and opening remarks
SESSION 1: Phages
Host: Anca Segall
09:30 — 10:00 The promise and pitfalls of prophages
Robert Edwards | Flinders University, Adelaide, Australia
10:00 — 10:20 Jaeger: A Deep Learning Approach for Predicting Bacteriophage Sequences in Metagenomic Data
Rajitha Yasas Wijesekara | University Medicine Greifswald, Greifswald, Germany
10:20 — 11:00 COFFEE BREAK
SESSION 2: Virus discovery and classification
Host: Justine Charon
11:00 — 11:10 RdRp Summit: outcomes
11:10 — 11:30 Illuminating the RNA Virome through ultra-massive sequence analysis
Artem Babaian | University of Toronto, Toronto, Canada
11:30 — 11:50 RNA virus discovery using HMM of large-scale RNA-dependent RNA polymerase sequence data: NeoRdRp 2.0
Shoichi Sakaguchi | Osaka Medical and Pharmaceutical University, Osaka, Japan
11:50 — 12:10 Automated classification of giant virus genomes using protein family barcodes
Anh Ha | Virginia Tech, Biological Sciences, Blacksburg, USA
12:10 — 12:30 Using gb2seq to work with unannotated viral genomes based on a GenBank reference
Terry Jones | Charité Universitätsmedizin, Berlin, Germany
12:30 — 14:00 LUNCH BREAK
SESSION 3: Virus visualization
Host: Manja Marz
14:00 — 14:30 Advanced optical microscopy of virus-cell interactions: challenges and potentials
Christian Eggeling | Friedrich‐Schiller‐University & Leibniz Institute of Photonic Technology e.V., Jena, Germany
14:30 — 15:30 Poster Session A
15:30 — 16:10 COFFE BREAK
SESSION 4: Viral infection
Host: Anamarija Butkovic
16:10 — 16:40 SARS-CoV-2-host interactions at the single-cell level: a dynamical complex systems approach
Santiago F. Elena | CSIC-Universitat de València, Valencia, Spain
16:40 — 17:00 Metabolic labeling, time series, and single cells: a multifaceted approach to studying infection
Lygeri Sakellaridi | University of Würzburg, Würzburg, Germany
SESSION 5: Viromics
Host: Spyros Lytras
17:00 — 17:20 Ancient virome analyses using metagenomic data from ancient individuals
Luca Nishimura | National Institute of Genetics, Mishima, Japan
17:20 — 17:40 One’s Trash is Another’s Treasure – Mining viromics datasets for traces of EV mediated horizontal gene transfer
Dominik Lücking | Max Planck Institute for Marine Microbiology, Bremen, Germany

Thursday, May 25

09:15 — 09:30 Announcements
SESSION 6: Molecular epidemiology and phylodynamic analyses
Host: Francesca Young
09:30 — 10:00 HIV-1 transmission studies using phylogenetics: can evolution help guide public health decisions?
Ana Abecasis | Universidade Nova de Lisboa, Lisbon, Portugal
10:00 — 10:30 Molecular epidemiological approaches to investigate the dispersal dynamic of viruses and the environmental factors impacting it
Simon Dellicour | Université Libre de Bruxelles, Bruxelles, Belgium
10:30 — 10:50 Phylodynamic analysis of A(H5N1) highly pathogenic avian influenza viruses provides insight into movement dynamics and host specificity
Will Harvey | University of Edinburgh, Edinburgh, United Kingdom
10:50 — 11:30 COFFEE BREAK
SESSION 7: RNA viruses: structure and evolution
Host: Dmitrij Frishman
11:30 — 12:00 Viral RNA secondary structures: canonical and beyond
Kevin Lamkiewicz & Sandra Triebel | Friedrich Schiller University Jena, Jena, Germany
12:00 — 12:20 Recombination and Modular Evolution of Positive-strand RNA Viruses: Similar, but not the Same
Yulia Vakulenko | Sechenov First Moscow State Medical University, Moscow, Russia
12:20 — 12:40 RNAswarm: A Modular Pipeline for Differential RRI Analysis in Influenza A Virus
Gabriel Lencioni Lovate | Friedrich Schiller University Jena, Jena, Germany
12:40 — 14:10 LUNCH BREAK
14:10 — 15:00 EVBC Meeting
15:00 — 16:00 Poster Session B
16:00 — 16:30 COFFE BREAK
SESSION 8: Viral sequence analysis
Host: Anne Kupczok
16:30 — 16:50 Embedding segmented viral genomes for visualisation, search, and clustering
Udo Gieraths | Charité — Universitätsmedizin Berlin, Virologie, Berlin
16:50 — 17:10 Hyper-EINS: A tool for automated identification of insertions in the hepatitis E virus hypervariable region
Maximilian Nocke | Ruhr University Bochum, Bochum, Germany
17:10 — 17:30 Magnipore: Predicting differential single nucleotide changes in Oxford Nanopore Technologies sequencing signal in SARS-CoV-2
Jannes Spangenberg | Friedrich Schiller University Jena, Jena, Germany
17:30 — 17:50 VILOCA: Sequencing quality-aware haplotype reconstruction and mutation calling for short- and long-read data
Lara Fuhrmann | ETH Zurich, Basel, Switzerland
20:00 Conference Dinner

Friday, May 26

09:15 — 09:30 Announcements
SESSION 9: Machine learning in viral surveillance
Host: Ingrida Olendraite
09:30 — 10:00 From High-Throughput Testing to Genomic Surveillance and Public Health Data Integration
Bernhard Renard | Hasso Plattner Institute, Potsdam, Germany
10:00 — 10:20 BLOODVIR: Virus surveillance system for plasma pools based on high-throughput sequencing and machine learning
Martin Machyna | Paul-Ehrlich-Institut, Langen, Germany
10:20 — 10:40 Modelling the zoonotic capabilities of avian influenza via genomic machine learning
Liam Brierley | University of Liverpool, Liverpool, UK
10:40 — 11:10 COFFEE BREAK
SESSION 10: Viral pathogenesis
Host: Jenna Kelly
11:10 — 11:40 Sex differences in avian influenza virus infections
Gülsah Gabriel | Leibniz Institute of Virology, Hamburg, Germany
11:40 — 12:40 Poster Session C
12:40 — 14:10 LUNCH BREAK
SESSION 11: Metagenomics for Identifying and Tracking Potential Zoonotic Viruses
Host: Jelle Matthijnssens
14:10 — 14:40 Metagenomic next generation sequencing as a tool for identifying undiagnosed pathogens
Emma Thomson | University of Glasgow, Glasgow, United Kingdom
14:40 — 15:00 Discovering and tracking potential zoonotic species from metagenomic samples with a capture-based oriented pipeline
Maria Tarradas-Alemany | Universitat de Barcelona, Barcelona, Spain
15:00 — 15:30 Closing ceremony / awards

Poster Sessions

Poster Session A

A01Data mining-based discovery and genomic characterization of novel tobamoviruses
Katarina Bačnik | National institute of biology, Ljubljana , Slovenia
A02RNA virus discovery in multiple mosquito species in Cambodia
Artem Baidaliuk | Institut Pasteur, Paris, France
A03Avitombusviridae: a new viral subfamily in birds
Yannick Blanchard | Anses, Ploufragan, France
A04A Tale of Caution: Endogenous viral elements might bias virus discovery in transcriptomic datasets
Nadja Brait | University of Groningen, Groningen, Netherlands
A05Virus Discovery using CZ ID — A free, Open Source, Cloud-based Metagenomics Platform for Researchers
Elizabeth Fahsbender | Chan Zuckerberg Initiative, Redwood City, USA
A06Optimization of Virome Enrichment Method of Human Respiratory Samples
Lisa Faye | KU Leuven, Leuven, Belgium
A07Studying the gut virome in shotgun metagenomic data from the Lifelines NEXT cohort
Asier Fernández-Pato | University Medical Center Groningen, Groningen, The Netherlands
A08Comparison of MERS-CoV infection in human and camelid primary airway epithelial cells with single-cell resolution
Vera Flück | University of Berne, Bern, Schweiz
A09Characterization of phages integrated into the genomes of cultured Faecalibacterium strains reveals diversity-generating retroelements targeting multiple genes
Anastasia Gulyaeva | University Medical Center Groningen, Groningen, The Netherlands
A10Utilising publicly available transcriptomic data to reveal the viromes of endangered species
Erin Harvey | The University of Sydney, Sydney, Australia
A11Preliminary results of taxonomic classification of virus sequences in biting midges from Western Aegean Region of Turkiye.
B. Taylan Koc | Friedrich Schiller University Jena, Jena, Germany
A12Finding a needle in a haystack: separating specific antiviral responses from general stress responses from transcriptomic data of Arabidopsis thaliana
Wilberth Lasso Giraldo | Universitat de València, València, Spain
A13International Committee on Taxonomy of Viruses (ICTV): Virus Classification and Nomenclature
Elliot Lefkowitz | University of Alabama Birmingham, Birmingham, USA
A14Viral acetyltransferases: a novel, yet widespread host-hijacking strategy in Pseudomonas phages
Hannelore Longin | KU Leuven, Leuven, Belgium
A15Longitudinal Metagenomic Analysis of Aedes Mosquito Virome in Cameroon
Karelle Celes Mbigha Donfack | KU Leuven, Leuven, Belgium
A16First description of a Polyomavirus genome in the Thornback ray (Raja clavata)
Fabiana Neves | CIBIO-InBio, Vairão – Vila do Conde, Portugal
A17Expansion of a novel RNA virus family: lessons from five years of Polycipiviridae
Ingrida Olendraite | University of Cambridge, Cambridge, United Kingdom
A18Crosstalk between virus accumulation and host responses in the C. elegans-Orsay virus pathosystem
María José Olmo Uceda | Institute for Integrative Systems Biology, I2SysBio (CSIC-UV), Paterna, Spain
A19Exploring the gut microbiota dynamics in healthy Bangladeshi infants: An insight into the gut virome development in early life.
Maria Ioanna Papadaki | KU Leuven, Leuven, Belgium
A20Viromics from Cryosphere lake sediments: adaptation to anoxic environments and identification of ancient viruses.
Sergio Sánchez Carrillo | Centro de Biología Molecular Severo Ochoa, Madrid, Spain
A21Computational processing of public sequencing files to identify clusters in high-dimensional human virome data
Josefin Säurich | University of Veterinary Medicine, Hannover, Germany
A22Dissecting viral diversity in the North Sea
Hisham Mohammed Shaikh | Flanders Marine Institute; Ghent University, Oostende, Belgium
A23Generic Ensembles in RdRp Modules on the Anvil of Evolution – Conformational Heterogeneity and Liquid Condensed States Modulate The Sequence-Ensembles Nature of RdRp Tethered Folded Domains
Rachid TAHZIMA | University of Liège, Gembloux, Belgium
A24The fecal virome in patients with alcoholic liver disease
Lore Van Espen | KU Leuven, Leuven, Belgium
A25Benchmarking Bioinformatic Virus Identification Tools Using Real Metagenomic Data across Biomes
Lingyi Wu | Utrecht University, Utrecht, Netherlands

Poster Session B

B01SLiM pickings: short linear motifs in viral genomes in viral genomes predict reservoir host as a function of viral phylogeny
Matt Arnold | University of Glasgow, Glasgow, United Kingdom
B02Genetic characterization of watermelon mosaic virus
Karima Ben Mansour | Czech University of Life Sciences, Prague, Czech Republic 
B03Viral community genomic variation in coral symbioses across Pacific Ocean island systems
Kalia Bistolas | Oregon State University, Corvallis, OR, USA 
B04Nanopore sequencing for bacterial mobilome characterization
Tibor Botka | Masaryk University, Brno, Czech Republic 
B05Evolution of anelloviruses from a circovirus-like ancestor through gradual augmentation of the jelly-roll capsid protein
Anamarija Butkovic | Institut Pasteur, Paris, France
B06Evolution of the interactions between rotavirus VP8* and histo-blood group antigens: Insights from computational studies
Roberto Cárcamo | Universitat de Valencia, Valencia, Spain 
B07Phylogenetic Conservation Scores to Select Primers for RHDV Identification
Filipa Carneiro | University of Porto, Porto, Portugal
B08Gsub: submitting a large number of viral sequences to GenBank in a easy and fast way
Florian Charriat | CIRAD, Montpellier, France
B09VILOCA: Sequencing quality-aware haplotype reconstruction and mutation calling for short- and long-read data
Lara Fuhrmann | ETH Zurich, Basel, Switzerland
B10Structural and evolutionary constraints on viral movement proteins encoded by overlapping genes in viral genomes
Esmeralda García Legarda | I2SysBio (CSIC), Valencia, Spain
B11Using network analysis for clustering OTUs in eukaryotic viromes
Serafin Gutierrez | CIRAD, Montpellier, France
B12Accumulation Dynamics of DVGs During Experimental Evolution of Betacoronaviruses
Julia Hillung | I2SysBio-CSIC, Valencia, Spain
B13Assessing methods for virus discovery in natural plant ecosystems
Dimitris Karapliafis | Wageningen University & Research, Wageningen, Netherlands
B14Ancient gene transfer links the early evolution of eukaryotes and giant viruses.
Sangita Karki | Virginia polytechnic institute and state university, Blacksburg, USA
B15An evolutionary perspective on RNA-protein interactions: Co-Alignments of an Ebolavirus RPI
Sarah Krautwurst | Friedrich Schiller University Jena, Jena, Germany
B16Co-transfer of functionally interdependent genes contributes to genome mosaicism in lambdoid phages
Anne Kupczok | Wageningen University and Research, Wageningen, Netherlands
B17RNAswarm: A Modular Pipeline for Differential RRI Analysis in Influenza A Virus
Gabriel Lencioni Lovate | Friedrich Schiller University Jena, Jena, Deutschland
B18In silico proteome-wide analysis of viral sequences reveals a potential for a novel chaperone-mediated xenophagy pathway
Marcin Lubocki | University of Gdańsk, Gdańsk, Poland
B19NGS-aided sequencing for plant viruses
Rebeka Ludviga | Latvian Biomedical Research and Study Centre, Riga, Latvia 
B20Gene transfer between mycoviruses and their hosts: the coat protein as a case study
Ayoub Maachi | Institute for Integrative Systems Biology, Valencia, Spain
B21Pan-family genomic survey of Potyviridae uncovers AlkB and N6-methyladenosine roles in plant infection
Fabio Pasin | Spanish National Research Council (CSIC), VALENCIA, Spain
B22Structure Conservation in Viral Polymerases
Olve Peersen | Colorado State University, Fort Collins, USA
B23Non-retroviral RNA viruses integrated into the human genome
Muriel Ritsch | Friedrich Schiller University Jena, Jena, Germany
B24VirJenDB: a comprehensive virus genome database
Shahram Saghaei | Friedrich Schiller University Jena, Jena, Germany
B25Molecular evolution of coxsackievirus A9 with a hint of receptor tropism – from VP1 to genome-sequencing.
Petri Susi | University of Turku, Turku, Finland
B26Genomic GC% Content Relationships Between Bacteriophages And Their Hosts
Nikita Zrelovs | Latvian Biomedical Research and Study Centre, Riga, Latvia

Poster Session C

C01Combinatorial analysis of deletion repair in SARS-CoV-2 variants of concern
Miguel Álvarez-Herrera | Institute for Integrative Systems Biology (UVEG-CSIC), Paterna, Valencia, Spain
C02Towards assessing the spillover potential of 3K novel negative-stranded RNA viruses.
Liubov Chuprikova | German Cancer Research Center (DKFZ), Heidelberg, Germany
C03Exploration of the Culex mosquito virome and its effect on West Nile and Usutu virus transmission
Lander De Coninck | KU Leuven, Leuven, Belgium
C04Virus-host interactions in Arctic tundra soils
Tatiana Demina | University of Helsinki, Helsinki, Finland
C05Metatranscriptomic approach for the analysis of viral diversity in Amazonian Mosquitoes
Eddie Fuques | Oregon State University, Corvallis, Oregon, United States 
C06Migration history of SARS-CoV-2 variants in Galicia, NW Spain
Pilar Gallego-García | Universidade de Vigo, Vigo, Spain
C07Viral Metagenomics from different regions of the Cryosphere
Rafael Gonzalez-Serrano | Spanish National Research Council (CSIC), Madrid, Spain
C08Leveraging Distributed Databases To Monitor Viral Detection Assays
Norman Hassell | Centers For Disease Control and Prevention, Atlanta, GA, United States
C09A deep sequencing strategy for investigation of virus variants within ASFV infected pigs
Camille Melissa Johnston | Statens Serum Institut, Copenhagen, Denmark
C10CZ ID – A Free, Open Source, Cloud-based Tool for Metagenomic Pathogen Detection and Monitoring
Katrina Kalantar | Chan Zuckerberg Initiative, Redwood City, USA
C11Mechanistic Insights into SARS-CoV-2 Main Protease Inhibition Reveals Hotspot Residues
Konda Reddy Karnati | Bowie State University, Bowie, Maryland, United States of America
C12Modeling influenza HA protein structures circulating during the 2022-2023 northern hemisphere season
Nicholas Kovacs | US Centers for Disease Control and Prevention, Atlanta, USA
C13Characterising the mutational landscape of SARS-CoV-2 using large language models
Kieran Lamb | University of Glasgow, Glasgow, United Kingdom
C14Prediction of virus-host association using protein language models and multiple instance learning
Dan Liu | University of Glasgow, Glasgow, United Kingdom
C15Patterns of Influenza Diversity in a Pilot Study of US Traveler Based Genomic Surveillance.
Sandra Mathew | CDC, Atlanta, United States
C16Genomic diversity of SARS-CoV-2 can be accelerated by mutations in the nsp14 gene
So Nakagawa | Tokai University School of Medicine, Isehara, Japan
C17Detection of co-infection events and the emergence of novel recombinants in the Epidemiological Surveillance of Andalusia (Spain)
Javier Perez-Florido | Computational Medicine Platform, Fundación Progreso y Salud, Seville, Spain
C18Within-patient SARS-CoV-2 adaptive mutations.
Sara Puchades-Sangabino | I2SYSBIO (UV-CSIC), Paterna (Valencia), Spain
C19Virome approach to the pathogen surveillance of wastewaters
Ana Abecasis | Universidade Nova de Lisboa, Lisbon, Portugal
C20Tracking intra host evolution of SARS-CoV-2
Jordi Sevilla | Institute for Integrative Systems Biology (UVEG-CSIC), Valencia, Spain
C21Temporal rank dynamics of transcripts in SARS-CoV-2-infected cells
João Silva | Instituto de Biología Integrativa de Sistemas, Paterna (Valencia), Spain
C22Integrative Analysis of Amplicon Coverage to Monitor the Performance of the Swift Amplicon SARS-CoV-2 Panel during the Evolution of Omicron
Xiao-yu “Sherry” Zheng | Center for Disease Control and Prevention, Atlanta GA, USA
C23Rapid whole genome amplification and sequencing protocol for Mpox Virus
Matthias Licheri | University of Bern, Bern, Switzerland


We would like to thank our sponsors for supporting the International Virus Bioinformatics Meeting 2023!