Our research uses genomics to understand viral diversity, evolution, emergence and transmission. Our work spans fundamental studies of virus evolution and discovery through to genomic investigations of emerging infectious diseases and outbreaks in Australia.
Eden J-S, et al. (2013). Recombination within the pandemic norovirus GII.4 lineage. Journal of Virology 87:6270–6282. Using genome-scale evolutionary analysis, we showed how recombination has repeatedly reshaped pandemic GII.4 noroviruses, identifying hotspots associated with the emergence of new variants. Link.
Shi M, Lin X-D, Chen X, Tian J-H, et al. (2018). The evolutionary history of vertebrate RNA viruses. Nature 556:197–202. A large-scale exploration of RNA virus diversity across vertebrates, revealing how host evolution and ecology have shaped the origins and long-term evolution of the vertebrate RNA virome. Link.
Eden J-S, Chisholm RH, et al. (2017). Persistent infections in immunocompromised hosts are rarely sources of new pathogen variants. Virus Evolution 3:vex018. Combining within-host evolution with epidemiological modelling, we explored whether prolonged infections in immunocompromised hosts disproportionately contribute to viral evolution and the emergence of new variants. Link.
Hurley S, Eden JS, et al. (2023). Fatal human neurologic infection caused by pigeon avian paramyxovirus-1, Australia. Emerging Infectious Diseases 29:2482–2487. A striking example of the power of genomic pathogen discovery: metagenomic sequencing helped identify pigeon avian paramyxovirus-1 as the cause of a fatal neurological infection in an immunocompromised child. Link.
Annand EJ, Horsburgh BA, et al. (2022). Novel Hendra virus variant detected by sentinel surveillance of horses in Australia. Emerging Infectious Diseases 28:693–704. The discovery of a highly divergent Hendra virus genotype from a fatal equine case revealed an important blind spot in existing diagnostic surveillance and expanded the known genetic and geographic diversity of Hendra virus in Australia. Link.
Yinda CK, Eden J-S, Prates ET, et al. (2026). Spatio-temporal dynamics of Hendra virus in Australia reveal stable maintenance of diverse viral clades among Pteropus bats. Nature Microbiology 11:851–866. Combining extensive viral genomics with longitudinal ecological surveillance, we revealed the remarkable diversity and long-term maintenance of Hendra virus lineages within Australian flying fox populations. Link.
Peel AJ, Ruiz-Aravena M, Kim K, et al. (2025). Synchronized seasonal excretion of multiple coronaviruses coincides with high rates of coinfection in immature bats. Nature Communications 16:6579. Longitudinal surveillance of Australian flying foxes revealed six co-circulating coronavirus clades, pronounced seasonal patterns of viral shedding and frequent coinfections, providing new insights into the ecology and evolution of bat coronaviruses. Link.
Eden J-S, Neave M, Smith C, Batovska J, et al. (2025). Emergence and spread of Japanese encephalitis virus genotype IV in a novel ecosystem: Australia, 2021–2022. [Preprint]. A national One Health genomic investigation of Australia’s unprecedented Japanese encephalitis outbreak, using 166 viral genomes from humans, mosquitoes, farmed pigs and feral pigs to reconstruct the emergence and rapid dispersal of JEV genotype IV across the continent. Link.
Eden J-S, Sikazwe C, Xie R, et al. (2022). Off-season RSV epidemics in Australia after easing of COVID-19 restrictions. Nature Communications 13:2884. Genomic surveillance revealed how Australia’s normal RSV ecology was profoundly disrupted during the COVID-19 pandemic, with reduced viral diversity, cryptic persistence and the subsequent emergence of large, unusual summer epidemics. Link.
Eden J-S, et al. (2020). An emergent clade of SARS-CoV-2 linked to returned travellers from Iran. Virus Evolution 6:veaa027. Published during the earliest months of the COVID-19 pandemic, this study used rapid whole-genome sequencing and phylogenetics to identify a distinct SARS-CoV-2 lineage associated with travellers returning from Iran to Australia and New Zealand, demonstrating the immediate value of genomic epidemiology during an emerging pandemic. Link.