Research Programme

Mind the gap: Paving the way with innovative tools developed in VirusREvolution

Building upon the community-driven structures and extensive preliminary work outlined above, we now summarise the key challenges that arose from our long-standing interactions with the international virus research community, including activities coordinated through the EVBC. These challenges have guided the formulation of the research questions addressed in the CRC VirusREvolution and align closely with the expertise of researchers in Jena and selected partners.
We have identified and categorised three fundamental research areas in virology for which substantial bioinformatic and photonic tools are lacking, all of which are essential for robust risk assessment of (emerging) viruses:
1. tools for unravelling the intricacies of virus tropism
2. tools to decipher the virus infection potential, to pave the way for the prediction of pathogenicity
3. tools for the systematic characterisation of (novel) viruses

In order to tackle these fundamental research questions and their tool development, we will break these down into more precise research questions, for which tools are largely absent:

Virus tropism:
  • How can we efficiently map different haplotypes of a quasispecies to the biological entities of the virus?
  • Can we create a more reliable phylogeny of viruses based on a multidimensional space of attributes?
  • How can we improve the surveillance of viruses?
  • How can we systematically identify and quantify virus-host interaction determinants across different cell types and tissues?
  • What analytical frameworks are needed to link virus genetic or structural variation to changes in cell-type specificity?
  • Can we develop tools to merge microscopic images, molecular profiles, and biophysical signatures into unified models of tropism?
Virus infection potential and early steps toward virulence assessment:
  • To what extent can we physically sort viruses by their morphology?
  • Can we develop a tool to rapidly scan and detail the virus surface to determine virus-host interaction potential?
  • In what way can we visualise and explore molecular details in virus entry and uncoating?
  • Are there generic approaches for imaging viruses, with minimal labelling requirements?
  • How can we develop a tool to categorise the virus-host interactions?
  • Can we predict optimal antiviral compounds at the RNA and protein level?
  • What molecular or morphological features provide the earliest measurable indicators of infection potential?
  • How can we characterise and compare virus-induced host responses in a way that supports risk assessment?
  • Which computational approaches can combine genomic, photonic, and phenotypic data to make the first steps toward estimating the pathogenic potential of emerging viruses?
Systematic characterisation of (novel) viruses:
  • Can complete multiple genome sequence alignments and pangenomic approaches serve as a fundamental unit for downstream analysis tools, such as phylogenetic reconstruction tools?
  • Can we improve the characterisation of virus replication strategies by annotating their (sub)genomic features using novel data structures?
  • Will we be able to efficiently detect the core components of virus-specific host responses?
  • How can we generate comprehensive and scalable genomic representations (e.g., pangenomes, multi-genome alignments) that support downstream comparative analyses?
  • Which computational strategies allow robust annotation of (sub)genomic features across highly diverse virus taxa?
  • How to integrate photonic/sequencing-based measurements to obtain holistic molecular fingerprints of viruses?
Looking ahead, the future of virology lies in the ability to assess and mitigate the risk of emerging viruses at multiple stages of their infection cycle. This endeavour requires exploring both intrinsic and host-induced virus properties through novel methodological developments, enabling the first steps toward understanding pathogenic potential. Innovative tools and interdisciplinary approaches are essential to advance our preparedness and response to virus threats.