PhD Projects » ESR 1: Deciphering the RNA genome packaging code of influenza A viruses

Host institution:
Friedrich Schiller University Jena (FSU), Germany
Local supervisor:
Prof. Dr. Manja Marz (FSU Jena)
Local co-supervisor:
Prof. Dr. Andreas Henke (Jena University Hospital)
Project partner:
Work packages:
WP 1.4 Virus regulation
WP 2.1 Microevolution: Virus quasispecies
WP 2.2 Macroevolution: Natural selection of viruses

Currently, bioinformatical tools are not specifically designed for viruses. However, viruses bring unique features, which require specific bioinformatical tools to trace virus-host interaction. For example, the number of sequences in a quasispecies is massively high due to their high mutation rate, but only a few interact again with the host cells. Some viruses, such as IAV or as used by AG, are segmented RNA viruses, which urgently require tools with specific features: RNA viruses should include standardised secondary structure predictions, leading to RNA-RNA interaction prediction necessary for the packaging of segmented RNA viruses.

Therefore the precise aims of this project are

  • Development of a bioinformatical tool to predict RNA-RNA interactions as packaging signal for segmented viruses, such as IAV. The tool will also consider the 3D arrangement of the RNA molecules being essential to understand the nature of packaged viruses.
  • Development of a virus-specific full genome multiple sequence alignment algorithm to track the quasispecies. We will combine this tool with secondary structure information being available from literature and ESR 2 to build more accurate alignments.
  • Establishment of RNA-RNA interaction sets and more importantly non-interaction sets. The result will be used by ESR 2 to explore the reassortment space of IAVs. This understanding is essential for a prediction of future Flu outbreaks.
  • Application of the tool for at least 30 different viruses in other projects in VIROINF.