NWO-XS for Mathis Funk

May 5, 2022 The influenza genome presents insertion and deletion (indel) hotspots at which nucleotides are repeatedly inserted or deleted by the viral polymerase in independently evolving viruses. The mechanisms driving polymerase indel errors at these hotspots are unknown but they can have major impacts on virulence and immune escape, as can be seen in human influenza B viruses (IBV). Over the past 50 years, 9 nucleotides have repeatedly been inserted and deleted at an indel hotspot in the IBV hemagglutinin (HA) gene, the major target of the immune response. Recently there have been 4 independent deletion events in IBV HA leading to 4 new HA lineages which are poorly recognized by antibodies directed against older HAs. Viruses with HAs bearing these deletions quickly became dominant in the seasonal epidemics and influenza vaccine strains had to be updated to include this deletion.

Previous work from our group has shown that some influenza indel hotspots occur in the loop of predicted RNA stem-loop structures. In this project, I will study the role of these local RNA structures in indel-generation using a virus-free influenza RdRp replication system combined with a customized Circular Sequencing Next-generation Sequencing approach. This will allow me to eschew viral fitness biases and sequence each RNA molecule several times to detect even ultra-low frequency indels accurately. By comparing the indel profile and propensity of different RNA structure and sequences, I will be able to unveil the mechanism underlying indel-generation at influenza indel hotspots and improve our knowledge on how influenza viruses evolve.
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