Insights into viral RNA synthesis by the influenza A virus and SARS-CoV-2 RNA polymerases

Thesis

Influenza A virus and SARS-CoV-2 are RNA viruses which cause severe respiratory disease and death in humans. Both encode RNA-dependent RNA polymerases (RdRps), which are responsible for synthesising viral RNA as part of a larger complex of viral proteins; for influenza A virus this complex is called a ribonucleoprotein (RNP), and for SARS-CoV-2 the replication- transcription complex (RTC). In this work I elucidate mechanisms used by influenza A virus and SARS-CoV-2 to synthesise viral RNA.

I first present evidence that the influenza A virus RdRp maintains the structural integrity of RNPs during transcription by binding to the 3′ end of viral genomic RNA. I then go on to demonstrate that in order to initiate viral RNA synthesis, the influenza A virus RdRp requires trans-activation through dimerization. Furthermore, I show that the influenza A virus RdRp co-opts the host protein ANP32A to help it form a second structurally-distinct dimer, which has the role of encapsidating nascent viral RNA into progeny RNPs. Collectively, these findings allow me to present a more detailed molecular model for how influenza viral RNA is synthesised and assembled into new RNPs.

One role of the influenza A virus RNP is to hide highly immunogenic viral RNA from cellular innate immune receptors such as RIG-I. The SARS-CoV-2 RTC instead synthesises 7- methylguanosine (m⁷G)-capped viral RNA which does not activate RIG-I. In this work I also show that one of the domains in the SARS-CoV-2 RdRp is a guanylyltransferase enzyme, which resolves a missing link in the mechanism of coronavirus m⁷G cap synthesis. Together, these studies improve understanding of the diverse mechanisms used by RNA viruses to synthesise viral RNA, and identify multiple functionally important sites on the influenza A virus and SARS- CoV-2 RdRps which could be exploited for future antiviral strategies.

Authors: Walker, A

• DOI: 10.5287/ora-9ennqayev
• Type of award: DPhil
• Level of award: Doctoral
• Awarding institution: University of Oxford
• Language: English
• Keywords: virus; coronavirus; influenza; polymerase; SARS; RNA