By working with virologists, RNA biochemists, bioinformaticians, and mathematicians, we are able to explore how viruses use RNA to grow and cause disease.
The majority of human respiratory viruses encode their genome as RNA, including those that cause COVID-19 and Influenza. Unlike DNA, RNA can encode information and function in its structure as well as its sequence.
This feature is exploited by all RNA viruses in one way or another. Coronaviruses, for example, use RNA structures to regulate their own genome replication, as well as to interact with host ribosomes. Influenza viruses use RNA structure to control splicing of viral genes and to drive reassortment of their eight genomic segments — the process that gives rise to new pandemic strains. Much of the details about how RNA structures act (and interact) during infection remains unknown.
One particular challenge is that viral RNA structures must be determined empirically: RNA structure prediction algorithms are not accurate for RNAs >1kb, and both host- and virus-encoded RNA binding proteins (such as the nucleocapsid) alter the RNA folding energy landscape. Moreover, these ribonucleoprotein complexes are typically dynamic and pleomorphic (i.e. they do not adopt a regular structure), precluding structural analysis by crystallography or Cryo-EM.
Chemical RNA probing methods coupled with next-generation sequencing, however, permit determination of RNA structures in the context of live cells and intact virions. This approach allows us to build up an integrated picture of how viral RNA is structured and how it interacts with cellular and viral components.
By combining this information with molecular virology and cell biology, we are able to develop our understanding of how RNA viruses replicate. In particular, we focus on understanding features that are common to nearly every RNA virus:
- Genome Packaging: Viral RNA is recognised by the assembling viral structural components and selectively incorporated into nascent virions. In highly-segmented viruses (like influenza viruses and rotavirus), the process is further complicated by the need to bundle together the correct set of genome segments prior to packaging.
- Emergence of New Strains: Segmented viruses can ‘mix and match’ their genome segments, while others (such as coronaviruses) can recombine to acquire large amounts of new genetic material, leading to the emergence of new virus strains.
- Control of genome replication: Structured RNA elements act to regulate the viral RNA-directed RNA polymerase, which is responsible for replicating the viral genome. By definition, these RNA structures are dynamic and must alter behaviour and structure at different points in the virus lifecycle.