The evolutionary mechanisms that drive pathogen emergence and spread. This work combines high-throughput sequencing and comparative genomics to explore the patterns of genetic variation, evolution and molecular epidemiology of clinically important viruses including norovirus, influenza virus and respiratory syncytial virus, as well as, other zoonotic and vector-borne diseases such as ross river virus. The aim of this research is to provide insights into the sources and mechanisms of how viral pathogens emerge, spread and evolve, not only at population scales but also within individual hosts, particularly in the context of infections in immunocompromised hosts. Another important focus of this research has been to better define the link between virus genetics (genotype) and infection outcome (phenotype) including the evolution of important traits such as virulence, drug-resistance and host range.
Unbiased sequencing for pathogen discovery. Recent work has focused on the application of meta-transcriptomics (total RNA sequencing) for pathogen discovery particularly in complex, undiagnosed human infections and in neglected wildlife disease outbreaks. The aim of this research is to develop robust sampling, sequencing and analytical approaches that can provide an unbiased snapshot of all microorganisms (virus, bacteria, fungi or parasite) present in a sample to aid in the diagnoses of infectious diseases, better understand microbial interactions and discovery new microbial diversity. A priority for this work is in the development of novel computational approaches to sort and annotate complex metagenomic datasets, so keen and interested bioinformatics students are encouraged to get in touch about joining the group.