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.

Awardees

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

A01	Data mining-based discovery and genomic characterization of novel tobamoviruses Katarina Bačnik | National institute of biology, Ljubljana , Slovenia
A02	RNA virus discovery in multiple mosquito species in Cambodia Artem Baidaliuk | Institut Pasteur, Paris, France
A03	Avitombusviridae: a new viral subfamily in birds Yannick Blanchard | Anses, Ploufragan, France
A04	A Tale of Caution: Endogenous viral elements might bias virus discovery in transcriptomic datasets Nadja Brait | University of Groningen, Groningen, Netherlands
A05	Virus Discovery using CZ ID — A free, Open Source, Cloud-based Metagenomics Platform for Researchers Elizabeth Fahsbender | Chan Zuckerberg Initiative, Redwood City, USA
A06	Optimization of Virome Enrichment Method of Human Respiratory Samples Lisa Faye | KU Leuven, Leuven, Belgium
A07	Studying the gut virome in shotgun metagenomic data from the Lifelines NEXT cohort Asier Fernández-Pato | University Medical Center Groningen, Groningen, The Netherlands
A08	Comparison of MERS-CoV infection in human and camelid primary airway epithelial cells with single-cell resolution Vera Flück | University of Berne, Bern, Schweiz
A09	Characterization 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
A10	Utilising publicly available transcriptomic data to reveal the viromes of endangered species Erin Harvey | The University of Sydney, Sydney, Australia
A11	Preliminary 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
A12	Finding 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
A13	International Committee on Taxonomy of Viruses (ICTV): Virus Classification and Nomenclature Elliot Lefkowitz | University of Alabama Birmingham, Birmingham, USA
A14	Viral acetyltransferases: a novel, yet widespread host-hijacking strategy in Pseudomonas phages Hannelore Longin | KU Leuven, Leuven, Belgium
A15	Longitudinal Metagenomic Analysis of Aedes Mosquito Virome in Cameroon Karelle Celes Mbigha Donfack | KU Leuven, Leuven, Belgium
A16	First description of a Polyomavirus genome in the Thornback ray (Raja clavata) Fabiana Neves | CIBIO-InBio, Vairão – Vila do Conde, Portugal
A17	Expansion of a novel RNA virus family: lessons from five years of Polycipiviridae Ingrida Olendraite | University of Cambridge, Cambridge, United Kingdom
A18	Crosstalk 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
A19	Exploring 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
A20	Viromics from Cryosphere lake sediments: adaptation to anoxic environments and identification of ancient viruses. Sergio Sánchez Carrillo | Centro de Biología Molecular Severo Ochoa, Madrid, Spain
A21	Computational processing of public sequencing files to identify clusters in high-dimensional human virome data Josefin Säurich | University of Veterinary Medicine, Hannover, Germany
A22	Dissecting viral diversity in the North Sea Hisham Mohammed Shaikh | Flanders Marine Institute; Ghent University, Oostende, Belgium
A23	Generic 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
A24	The fecal virome in patients with alcoholic liver disease Lore Van Espen | KU Leuven, Leuven, Belgium
A25	Benchmarking Bioinformatic Virus Identification Tools Using Real Metagenomic Data across Biomes Lingyi Wu | Utrecht University, Utrecht, Netherlands

Poster Session B

B01	SLiM 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
B02	Genetic characterization of watermelon mosaic virus Karima Ben Mansour | Czech University of Life Sciences, Prague, Czech Republic
B03	Viral community genomic variation in coral symbioses across Pacific Ocean island systems Kalia Bistolas | Oregon State University, Corvallis, OR, USA
B04	Nanopore sequencing for bacterial mobilome characterization Tibor Botka | Masaryk University, Brno, Czech Republic
B05	Evolution of anelloviruses from a circovirus-like ancestor through gradual augmentation of the jelly-roll capsid protein Anamarija Butkovic | Institut Pasteur, Paris, France
B06	Evolution of the interactions between rotavirus VP8* and histo-blood group antigens: Insights from computational studies Roberto Cárcamo | Universitat de Valencia, Valencia, Spain
B07	Phylogenetic Conservation Scores to Select Primers for RHDV Identification Filipa Carneiro | University of Porto, Porto, Portugal
B08	Gsub: submitting a large number of viral sequences to GenBank in a easy and fast way Florian Charriat | CIRAD, Montpellier, France
B09	VILOCA: Sequencing quality-aware haplotype reconstruction and mutation calling for short- and long-read data Lara Fuhrmann | ETH Zurich, Basel, Switzerland
B10	Structural and evolutionary constraints on viral movement proteins encoded by overlapping genes in viral genomes Esmeralda García Legarda | I2SysBio (CSIC), Valencia, Spain
B11	Using network analysis for clustering OTUs in eukaryotic viromes Serafin Gutierrez | CIRAD, Montpellier, France
B12	Accumulation Dynamics of DVGs During Experimental Evolution of Betacoronaviruses Julia Hillung | I2SysBio-CSIC, Valencia, Spain
B13	Assessing methods for virus discovery in natural plant ecosystems Dimitris Karapliafis | Wageningen University & Research, Wageningen, Netherlands
B14	Ancient gene transfer links the early evolution of eukaryotes and giant viruses. Sangita Karki | Virginia polytechnic institute and state university, Blacksburg, USA
B15	An evolutionary perspective on RNA-protein interactions: Co-Alignments of an Ebolavirus RPI Sarah Krautwurst | Friedrich Schiller University Jena, Jena, Germany
B16	Co-transfer of functionally interdependent genes contributes to genome mosaicism in lambdoid phages Anne Kupczok | Wageningen University and Research, Wageningen, Netherlands
B17	RNAswarm: A Modular Pipeline for Differential RRI Analysis in Influenza A Virus Gabriel Lencioni Lovate | Friedrich Schiller University Jena, Jena, Deutschland
B18	In silico proteome-wide analysis of viral sequences reveals a potential for a novel chaperone-mediated xenophagy pathway Marcin Lubocki | University of Gdańsk, Gdańsk, Poland
B19	NGS-aided sequencing for plant viruses Rebeka Ludviga | Latvian Biomedical Research and Study Centre, Riga, Latvia
B20	Gene transfer between mycoviruses and their hosts: the coat protein as a case study Ayoub Maachi | Institute for Integrative Systems Biology, Valencia, Spain
B21	Pan-family genomic survey of Potyviridae uncovers AlkB and N6-methyladenosine roles in plant infection Fabio Pasin | Spanish National Research Council (CSIC), VALENCIA, Spain
B22	Structure Conservation in Viral Polymerases Olve Peersen | Colorado State University, Fort Collins, USA
B23	Non-retroviral RNA viruses integrated into the human genome Muriel Ritsch | Friedrich Schiller University Jena, Jena, Germany
B24	VirJenDB: a comprehensive virus genome database Shahram Saghaei | Friedrich Schiller University Jena, Jena, Germany
B25	Molecular evolution of coxsackievirus A9 with a hint of receptor tropism – from VP1 to genome-sequencing. Petri Susi | University of Turku, Turku, Finland
B26	Genomic GC% Content Relationships Between Bacteriophages And Their Hosts Nikita Zrelovs | Latvian Biomedical Research and Study Centre, Riga, Latvia

Poster Session C

C01	Combinatorial analysis of deletion repair in SARS-CoV-2 variants of concern Miguel Álvarez-Herrera | Institute for Integrative Systems Biology (UVEG-CSIC), Paterna, Valencia, Spain
C02	Towards assessing the spillover potential of 3K novel negative-stranded RNA viruses. Liubov Chuprikova | German Cancer Research Center (DKFZ), Heidelberg, Germany
C03	Exploration of the Culex mosquito virome and its effect on West Nile and Usutu virus transmission Lander De Coninck | KU Leuven, Leuven, Belgium
C04	Virus-host interactions in Arctic tundra soils Tatiana Demina | University of Helsinki, Helsinki, Finland
C05	Metatranscriptomic approach for the analysis of viral diversity in Amazonian Mosquitoes Eddie Fuques | Oregon State University, Corvallis, Oregon, United States
C06	Migration history of SARS-CoV-2 variants in Galicia, NW Spain Pilar Gallego-García | Universidade de Vigo, Vigo, Spain
C07	Viral Metagenomics from different regions of the Cryosphere Rafael Gonzalez-Serrano | Spanish National Research Council (CSIC), Madrid, Spain
C08	Leveraging Distributed Databases To Monitor Viral Detection Assays Norman Hassell | Centers For Disease Control and Prevention, Atlanta, GA, United States
C09	A deep sequencing strategy for investigation of virus variants within ASFV infected pigs Camille Melissa Johnston | Statens Serum Institut, Copenhagen, Denmark
C10	CZ ID – A Free, Open Source, Cloud-based Tool for Metagenomic Pathogen Detection and Monitoring Katrina Kalantar | Chan Zuckerberg Initiative, Redwood City, USA
C11	Mechanistic Insights into SARS-CoV-2 Main Protease Inhibition Reveals Hotspot Residues Konda Reddy Karnati | Bowie State University, Bowie, Maryland, United States of America
C12	Modeling influenza HA protein structures circulating during the 2022-2023 northern hemisphere season Nicholas Kovacs | US Centers for Disease Control and Prevention, Atlanta, USA
C13	Characterising the mutational landscape of SARS-CoV-2 using large language models Kieran Lamb | University of Glasgow, Glasgow, United Kingdom
C14	Prediction of virus-host association using protein language models and multiple instance learning Dan Liu | University of Glasgow, Glasgow, United Kingdom
C15	Patterns of Influenza Diversity in a Pilot Study of US Traveler Based Genomic Surveillance. Sandra Mathew | CDC, Atlanta, United States
C16	Genomic diversity of SARS-CoV-2 can be accelerated by mutations in the nsp14 gene So Nakagawa | Tokai University School of Medicine, Isehara, Japan
C17	Detection 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
C18	Within-patient SARS-CoV-2 adaptive mutations. Sara Puchades-Sangabino | I2SYSBIO (UV-CSIC), Paterna (Valencia), Spain
C19	Virome approach to the pathogen surveillance of wastewaters Ana Abecasis | Universidade Nova de Lisboa, Lisbon, Portugal
C20	Tracking intra host evolution of SARS-CoV-2 Jordi Sevilla | Institute for Integrative Systems Biology (UVEG-CSIC), Valencia, Spain
C21	Temporal rank dynamics of transcripts in SARS-CoV-2-infected cells João Silva | Instituto de Biología Integrativa de Sistemas, Paterna (Valencia), Spain
C22	Integrative 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
C23	Rapid whole genome amplification and sequencing protocol for Mpox Virus Matthias Licheri | University of Bern, Bern, Switzerland

Sponsors

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