Bioinformatics Meets Virology: The European Virus Bioinformatics Center's Second Annual Meeting

Abstract

The Second Annual Meeting of the European Virus Bioinformatics Center (EVBC), held in Utrecht, Netherlands, focused on computational approaches in virology, with topics including (but not limited to) virus discovery, diagnostics, (meta-)genomics, modeling, epidemiology, molecular structure, evolution, and viral ecology. The goals of the Second Annual Meeting were threefold: (i) to bring together virologists and bioinformaticians from across the academic, industrial, professional, and training sectors to share best practice; (ii) to provide a meaningful and interactive scientific environment to promote discussion and collaboration between students, postdoctoral fellows, and both new and established investigators; (iii) to inspire and suggest new research directions and questions. Approximately 120 researchers from around the world attended the Second Annual Meeting of the EVBC this year, including 15 renowned international speakers. This report presents an overview of new developments and novel research findings that emerged during the meeting.

Keywords: bioinformatics; software; virology; viruses.

Figure 1

Hypothetical impact of indirect vector transmission on virus virulence evolution in Apis mellifera. The Varroa destructor reproductive life cycle is shown, with mites depicted at various developmental stages. A mother mite lays maximally three eggs that can mature to adulthood before hosts emerge from the brood cell. Virulence should evolve to an intermediate level that maximizes transmission (white region). Too virulent (red region) and the virus will have suboptimal transmission as a result of high host mortality preventing mite mating/host eclosion; not virulent enough (blue region) and the virus will have suboptimal transmission as a result of low growth (fewer transmission units). Reproduced with permission from McMahon, D.P.; Wilfert, L.; Paxton, R.J.; Brown, M.J.F. Emerging viruses in bees: from molecules to ecology. Adv. Virus. Res. 2018, in press. (https://doi.org/10.1016/bs.aivir.2018.02.008).

Figure 2

Workflow of TABAJARA program.

Figure 3

Number of shared samples with detected viruses (k_Viruses) in all three methods.

Figure 4

Comparison of predominant antigenic types for human influenza A/H3N2, predictions using sweep dynamics (SD) plots and recommendations made by the World Health Organization (WHO). The selection of a vaccine strain takes place two seasons before the vaccine is available. Any prediction of newly arising antigenically novel strains should therefore be compared to the predominant antigenic type two seasons later (indicated by diagonal lines in plot). (First row) Colored boxes indicate the predominant antigenic variant, and additional colored borders indicate different dominantly circulating strains matching the same antigenic variant; (Second row) For the SD plots’ analysis, seasons are marked with an “X” if sweep-related changes distinguish the WHO-selected vaccine strain from the previous strain. Seasons with sweep changes not associated with antigenicity-altering or avidity-changing sites are marked in grey; (Third row) Sweep-related changes in antigenicity-altering or avidity-changing sites. Using these as a criterion for vaccine strain updates results in a simultaneous or earlier detection of newly emerging antigenic types than with the procedure utilized by the WHO; (Fourth row) Detected sweep-related sites known to change neither the avidity nor the antigenicity; (Fifth row) WHO recommendations. Until 2017N, performance was evaluated by retrospective testing, in which data from after the time of the WHO vaccine strain meeting for a particular season was excluded from the analysis. From 2017S onwards, predictions were made for the future and can be monitored live at https://github.com/hzi-bifo/SDplots_VaccineUpdates.