The research training programme of VIROINF tackles major bioinformatical and virological challenges: the power of new genome sequencing technologies, associated with new tools to handle “big data”, provide unprecedented opportunities to address the fundamental questions in virology and virus-host interaction. Many of the common questions raised in virology require specific bioinformatics support and the combined expertise of both bioinformaticians and virologists.

WP 1: Modelling virus-host interactions

This work package aims at developing fundamental bioinformatical tools for modelling virus-host interactions and understanding these interactions mechanistically. In order to describe virus-host interactions (WP 1.3), interacting viruses need to be identified (WP 1.1) and hosts need to be determined (WP 1.2). The regulation of host by their viruses (WP 1.4) is the logical entity to establish viral products (WP 1.5) against their harmful hosts.

The VIROINF network involves the leading experts working with viruses infecting human, bird, mouse and pig (Influenza A virus, Cytomegalovirus), insects (honey bee virus, drosophila C virus, deformed wing virus) and microorganisms (mainly phages). This is complemented by the usage of new genomes sequencing techniques, new algorithms, wet-lab protocols and the establishment of a multiple layer database. Stars indicate cutting edge methods developed by our beneficaries. FSU runs the sequencing core facility and developed several virus-specific protocols for sequencing on Illumina and Minion.

WP 2: Modelling virus evolution in hosts

This work package aims at deciphering evolutionary forces shaping viral adaptation. To this end, virus evolution experiments will be performed in the lab, generating vast amounts of genomic and transcriptomic data. Sophisticated bioinformatical tools will be developed that allow us to recover the evolutionary dynamics and relate phenotypic attributes to evolved genetic material, to changes in the transcriptome structure and in the viral quasispecies composition.

VIROINF aims to develop tools for both established levels: In the area of microevolution (WP 2.1), the short term evolution (at most a few years) is examined in the viral population, also known as ‘virus quasispecies’. In the area of macroevolution (WP 2.2), the long term evolution (millions of years) is examined to determine the relation of virus families.