We are interested in fundamental aspects of the replication cycle of positive-strand RNA viruses - in particular the Picornaviruses and Hepatitis C virus. Our interests primarily focus on four areas:

1. The interaction of the virus with its cellular receptor. For these studies we concentrate upon the Enterovirus genus of the picornaviruses. This genus includes a large number of viruses that infect humans, causing a wide range of diseases - from hand, foot and mouth disease, to haemorrhagic conjunctivitis, myocarditis, diabetes and encephalitis. Our recent studies have focussed on the enteroviruses that bind decay accelerating factor (DAF), a GPI-linked protein expressed at the surface of most serum-exposed cells. DAF is complement control protein, involved in protecting autologous cells from complement-mediated destruction. Our work has involved the identification and characterisation of DAF as a virus receptor, the mapping of the virus-receptor interface (including collaborative studies that have determined the atomic structure of DAF, and the cryo-EM structure of the virus-receptor complex) and the dissection of the mechanism of virus entry.

Our current studies focus on the post-binding processes involved in virus entry, using a combination of bio-imaging, in vitro reconstitution and inhibitor studies.

2. The role of structured RNA elements in the replication of enteroviruses and Hepatitis C virus. RNA stem-loop structures have fundamental roles in the replication of many viruses. In the Picornaviridae the 5' and 3' non-coding regions (NCR) are heavily structured and have long been known to function during polyprotein translation or genome replication. Using rather primitive bioinformatic analysis we identified a short stem-loop structure located almost centrally in the poliovirus genome, and demonstrated it functioned as a cis-acting replication element (CRE). Disruption of the structure prevented replication, but function was not position-dependent. Subsequent studies have demonstrated that this CRE functions as the template for the uridylylation of VPg, the protein-nucleotide primer of virus replication. All picornaviruses possess a CRE, though the sequence, structure and location is not conserved.

Our current studies are focussing on the role of additional unstructured conserved RNA motifs - identified using novel bioinformatic approaches - which are also required for virus replication. 

3. Recombination in enteroviruses.  Enteroviruses exhibit high rates of recombination, a process that contributes significantly to the evolution of this group of pathogens.  We have recently started studies on the functional constraints that influence virus recombination, and the molecular determinants of the process.

4. Genome-scale ordered RNA structure. In collaborative studies with Prof. Peter Simmonds (University of Edinburgh) we have identified a novel characteristic exhibited by several genera of positive-strand plant and animal RNA viruses which we designate genome-scale ordered RNA structure (GORS). This feature - characterised by conserved levels of structured RNA without evolutionary conserved individual elements - is present in viruses that cause persisitent infections of immunocompetent hosts. Studies are underway to determine if this RNA structure has a role in modification, subversion or escape from innate immune responses of the host.