People_

Dr John-Sebastian Eden

Senior Research Fellow
Sydney Medical School Institutes / Westmead Institute for Medical Research

Phone

+61 2 8627 1817

Email

js.eden@sydney.edu.au

Details

Member of the Charles Perkins Centre

Websites

Google Scholar

Level 6 - Westmead Institute for Medical Research

Resume

Curriculum vitae

Biographical details

Dr John-Sebastian Eden is Research Scientist in Bioinformatics and Genomics based at the Westmead Insitute for Medical Research and Senior Research Fellow in the Sydney Medical School. Dr Eden is a Virologist, who joined the University of Sydney in 2013 with a post-doctoral position in the research group of Professor Eddie Holmes and supported by an NHMRC early career fellowship. Dr Eden has a strong background in viral genome sequencing and analysis, including the application of next-generation sequencing protocols and state-of-the-art bioinformatics methods.

Research interests

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.

Current projects

The evolution and molecular epidemiology of respiratory syncytial virus in Australia
Revealing transmission networks using genomics for viral respiratory infections
Metatranscriptomics for pathogen discovery
Bioinformatics and computational methods in pathogen genomics

A number of positions are available for both honours and HDR students. Please email if you are interested in working on any of these projects (js.eden@sydney.edu.au).

Associations

Centre for Virus Research at the Westmead Institute for Medical Reseach
Marie Bashir Institute for Infectious Diseases and Biosecurity
Biology Domain at the Charles Perkins Centre
Professional member of the Australian Society for Microbiology

Awards and honours

NHMRC Peter Doherty Early Career Fellowship (2014-18)

Themes

Infection and Immunological Conditions

Keywords

Bioinformatics, Computational biology, Virology

Current research students

Project title	Research student
Investigating the Effects of the Tuberculosis (TB)-Associated Microenvironment on HIV Persistence and CD8+ T-Cell-Mediated HIV Clearance	Samantha CRONIN
Novel Viruses in Australian Horses, Bats, and Wildlife, Understood Through Metatranscriptomics.	K9 JENNS

Publications

By Type

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Journals

Hurley, S., McMullan, B., Williams, D., Watson, J., Solinas, A., Kim, K., Rawlinson, W., Eden, J., Bingham, J., Rodriguez, M., Howard-Jones, A., et al (2023). Fatal Human Neurologic Infection Caused by Pigeon Avian Paramyxovirus-1, Australia. Emerging Infectious Diseases, 29(12), 2482-2487. [More Information]
Maamary, J., Maddocks, S., Barnett, Y., Wong, S., Rodriguez, M., Hueston, L., Jeoffreys, N., Eden, J., Dwyer, D., Floyd, T., et al (2023). New Detection of Locally Acquired Japanese Encephalitis Virus Using Clinical Metagenomics, New South Wales, Australia. Emerging Infectious Diseases, 29(3), 627-630. [More Information]
Horsburgh, B., Hiener, B., Fisher, K., Lee, E., Morgan, H., Eden, J., von Stockenstrom, S., Odevall, L., Milush, J., Hoh, R., Schlub, T., Palmer, S., et al (2022). Cellular Activation, Differentiation, and Proliferation Influence the Dynamics of Genetically Intact Proviruses over Time. The Journal of Infectious Diseases, 225(7), 1168-1178. [More Information]
Pham, D., Howard-Jones, A., Hueston, L., Jeoffreys, N., Doggett, S., Rockett, R., Eden, J., Sintchenko, V., Chen, S., O'Sullivan, M., Dwyer, D., et al (2022). Emergence of Japanese encephalitis in Australia: a diagnostic perspective. Pathology, 54(6), 669-677. [More Information]
Howard-Jones, A., Pham, D., Jeoffreys, N., Eden, J., Hueston, L., Kesson, A., Nagendra, V., Samarasekara, H., Newton, P., Chen, S., O'Sullivan, M., Dwyer, D., Kok, J., et al (2022). Emerging Genotype IV Japanese Encephalitis Virus Outbreak in New South Wales, Australia. Viruses, 14(9). [More Information]
Cole, B., Lambrechts, L., Boyer, Z., Noppe, Y., De Scheerder, M., Eden, J., Vrancken, B., Schlub, T., McLaughlin, S., Frenkel, L., Palmer, S., et al (2022). Extensive characterization of HIV-1 reservoirs reveals links to plasma viremia before and during analytical treatment interruption. Cell Reports, 39(4), 110739. [More Information]
Peel, A., Yinda, C., Annand, E., Dale, A., Eby, P., Eden, J., Jones, D., Kessler, M., Lunn, T., Schulz, J., et al (2022). Novel Hendra Virus Variant Circulating in Black Flying Foxes and Grey-Headed Flying Foxes, Australia. Emerging Infectious Diseases, 28(5), 1043-1047. [More Information]
Taylor, J., Thompson, K., Annand, E., Massey, P., Bennett, J., Eden, J., Horsburgh, B., Hodgson, E., Wood, K., Kerr, J., et al (2022). Novel variant Hendra virus genotype 2 infection in a horse in the greater Newcastle region, New South Wales, Australia. One Health, 15, Article number 100423-1-Article number 100423-7. [More Information]
Eden, J., Sikazwe, C., Xie, R., Deng, Y., Sullivan, S., Michie, A., Levy, A., Cutmore, E., Blyth, C., Britton, P., Dwyer, D., Horsburgh, B., Tulloch, R., Holmes, E., et al (2022). Off-season RSV epidemics in Australia after easing of COVID-19 restrictions. Nature Communications, 13(2884). [More Information]
Fisher, K., Wang, X., Lee, A., Morcilla, V., De Vries, A., Lee, E., Eden, J., Deeks, S., Kelleher, A., Palmer, S. (2022). Plasma-Derived HIV-1 Virions Contain Considerable Levels of Defective Genomes. Journal of Virology, 96(6), e0201121. [More Information]
Tulloch, R., Kok, J., Carter, I., Dwyer, D., Eden, J. (2021). An amplicon-based approach for the whole-genome sequencing of human metapneumovirus. Viruses, 13(3), 499-1-499-11. [More Information]
Eden, J. (2021). Genome sequencing and its use in public health responses to COVID-19. Microbiology Australia, 42(1), 44-46. [More Information]
Agius, J., Phalen, D., Rose, K., Eden, J. (2021). Genomic Insights Into the Pathogenicity of a Novel Biofilm-Forming Enterococcus sp. Bacteria (Enterococcus lacertideformus) Identified in Reptiles. Frontiers in Microbiology, 12, 635208. [More Information]
Lee, E., Sandgren, K., Duette, G., Stylianou, V., Khanna, R., Eden, J., Blyth, E., Gottlieb, D., Cunningham, A., Palmera, S. (2021). Identification of SARS-CoV-2 nucleocapsid and spike T-cell epitopes for assessing T-cell immunity. Journal of Virology, 95(6), 2002. [More Information]
Porter, A., Cobbin, J., Li, C., Eden, J., Holmes, E. (2021). Metagenomic identification of viral sequences in laboratory reagents. Viruses, 13(11), 2122. [More Information]
Robertson, M., Eden, J., Levy, A., Carter, I., Tulloch, R., Cutmore, E., Horsburgh, B., Sikazwe, C., Dwyer, D., Smith, D., et al (2021). The spatial-temporal dynamics of respiratory syncytial virus infections across the east–west coasts of Australia during 2016–17. Virus Evolution, 7(2), A1360. [More Information]
Ortiz-Baez, A., Eden, J., Moritz, C., Holmes, E. (2020). A Divergent Articulavirus in an Australian Gecko Identified Using Meta-Transcriptomics and Protein Structure Comparisons. Viruses, 12(6), 613. [More Information]
Eden, J., Rockett, R., Carter, I., Rahman, H., de Ligt, J., Hadfield, J., Storey, M., Ren, X., Tulloch, R., Basile, K., Sintchenko, V., Chen, S., Sorrell, T., Holmes, E., Dwyer, D., et al (2020). An emergent clade of SARS-CoV-2 linked to returned travellers from Iran. Virus Evolution, 6(1), veaa027. [More Information]
Bull, R., Adikari, T., Ferguson, J., Hammond, J., Stevanovski, I., Beukers, A., Naing, Z., Yeang, M., Verich, A., Gamaarachchi, H., Eden, J., Van Hal, S., et al (2020). Analytical validity of nanopore sequencing for rapid SARS-CoV-2 genome analysis. Nature Communications, 11(1), 1-8. [More Information]
Nguyen, T., Pham, T., Van, T., Nguyen, T., Ngoc Nguyen, D., Minh Le, H., Eden, J., Rockett, R., Hong Nguyen, T., Ngoc Vu, B., Dwyer, D., et al (2020). Genetic diversity of SARS-CoV-2 and clinical, epidemiological characteristics of COVID-19 patients in Hanoi, Vietnam. PloS One, 15, 1-15. [More Information]
Horsburgh, B., Lee, E., Hiener, B., Eden, J., Schlub, T., von Stockenstrom, S., Odevall, L., Milush, J., Liegler, T., Sinclair, E., Palmer, S., et al (2020). High levels of genetically intact HIV in HLA-DR+ memory T cells indicates their value for reservoir studies. AIDS, 34(5), 659-668. [More Information]
Tuddenham, R., Eden, J., Gilbey, T., Dwyer, D., Jennings, Z., Holmes, E., Branley, J. (2020). Human pegivirus in brain tissue of a patient with encephalitis. Diagnostic Microbiology and Infectious Disease, 96(2), 1-3. [More Information]
Rahman, H., Carter, I., Basile, K., Donovan, L., Kumar, S., Tran, T., Ko, D., Alderson, S., Sivaruban, T., Eden, J., O'Sullivan, M., Sintchenko, V., Chen, S., Dwyer, D., et al (2020). Interpret with caution: An evaluation of the commercial AusDiagnostics versus in-house developed assays for the detection of SARS-CoV-2 virus. Journal Of Clinical Virology, 127, 1-6. [More Information]
Ortiz-Baez, A., Cousins, K., Eden, J., Chang, W., Harvey, E., Pettersson, J., Carver, S., Polkinghorne, A., Slapeta, J., Rose, K., Holmes, E. (2020). Meta‑transcriptomic identification of Trypanosoma spp. in native wildlife species from Australia. Parasites and Vectors, 13(477), 1-10. [More Information]
Chang, W., Eden, J., Hall, J., Shi, M., Rose, K., Holmes, E. (2020). Meta-transcriptomic analysis of virus diversity in urban wild birds with paretic disease. Journal of Virology, 94(18), 1-22. [More Information]
Chang, W., Li, C., Hall, J., Eden, J., Hyndman, T., Holmes, E., Rose, K. (2020). Meta-transcriptomic discovery of a divergent circovirus and a chaphamaparvovirus in captive reptiles with proliferative respiratory syndrome. Viruses, 12(10), 1073. [More Information]
Turnbull, O., Ortiz-Baez, A., Eden, J., Shi, M., Williamson, J., Gaston, T., Zhang, Y., Holmes, E., Geohegan, J. (2020). Meta-Transcriptomic Identification of Divergent Amnoonviridae in Fish. Viruses, 12(11), 1-10. [More Information]
Porter, A., Pettersson, J., Chang, W., Harvey, E., Rose, K., Shi, M., Eden, J., Buchmann, J., Moritz, C., Holmes, E. (2020). Novel hepaci- and pegi-like viruses in native Australian wildlife and non-human primates. Virus Evolution, 6(2), 1-13. [More Information]
Vaz, F., Raso, T., Agius, J., Hunt, T., Leishman, A., Eden, J., Phalen, D. (2020). Opportunistic sampling of wild native and invasive birds reveals a rich diversity of adenoviruses in Australia. Virus Evolution, 6(1), 1-13. [More Information]
Basile, K., Habibur Rahman, H., Carter, I., Donovan, L., Kumar, S., Tran, T., Ko, D., Alderson, S., Sivaruban, T., Eden, J., Rockett, R., O'Sullivan, M., Sintchenko, V., Chen, S., Maddocks, S., Dwyer, D., Kok, J. (2020). Response. Journal Of Clinical Virology, 130, e19779. [More Information]
Rockett, R., Arnott, A., Lam, C., Sadsad, R., Timms, V., Gray, K., Eden, J., Chang, S., Gall, M., Draper, J., O'Sullivan, M., Chen, S., Sorrell, T., Dwyer, D., Holmes, E., Kok, J., Prokopenko, M., Sintchenko, V., et al (2020). Revealing COVID-19 transmission in Australia by SARS-CoV-2 genome sequencing and agent-based modeling. Nature Medicine, 26(9), 1398-1404. [More Information]
Phalen, D., Agius, J., Vaz, F., Eden, J., Setyo, L., Donahoe, S. (2019). A survey of a mixed species aviary provides new insights into the pathogenicity, diversity, evolution, host range, and distribution of psittacine and passerine adenoviruses. Avian pathology, 48(5), 437-443. [More Information]
Porter, A., Shi, M., Eden, J., Zhang, Y., Holmes, E. (2019). Diversity and Evolution of Novel Invertebrate DNA Viruses Revealed by Meta-Transcriptomics. Viruses, 11, 1-21. [More Information]
Harvey, E., Rose, K., Eden, J., Lo, N., Abeyasuriya, T., Shi, M., Doggett, S., Holmes, E. (2019). Extensive Diversity of RNA Viruses in Australian Ticks. Journal of Virology, 93(3), 1-15. [More Information]
Douglas, M., Tay, E., Eden, J., George, J. (2019). Hepatitis C Virus Genotype 8 - successful treatment with sofosbuvir/velpatasvir. The Journal of Infectious Diseases, 220(4), 720-722. [More Information]
Harvey, E., Rose, K., Eden, J., Lawrence, A., Doggett, S., Holmes, E. (2019). Identification of diverse arthropod associated viruses in native Australian fleas. Virology, 535, 189-199. [More Information]
Pettersson, J., Shi, M., Eden, J., Holmes, E., Hesson, J. (2019). Meta-transcriptomic comparison of the RNA Viromes of the mosquito vectors culex pipiens and culex torrentium in Northern Europe. Viruses, 11, 1-20. [More Information]
Marcelino, V., Wille, M., Hurt, A., Gonzalez-Acuna, D., Klaassen, M., Schlub, T., Eden, J., Shi, M., Iredell, J., Sorrell, T., Holmes, E. (2019). Meta-transcriptomics reveals a diverse antibiotic resistance gene pool in avian microbiomes. BMC Biology, 17(1), 1-11. [More Information]
Marcelino, V., Irinyi, L., Eden, J., Meyer, W., Holmes, E., Sorrell, T. (2019). Metatranscriptomics as a tool to identify fungal species and subspecies in mixed communities – a proof of concept under laboratory conditions. IMA Fungus, 10(1), 1-10. [More Information]
Agius, J., Phalen, D., Rose, K., Eden, J. (2019). New insights into Sauropsid Papillomaviridae evolution and epizootiology: discovery of two novel papillomaviruses in native and invasive Island geckos. Virus Evolution, 5(2), 1-12. [More Information]
Chang, W., Pettersson, J., Le Lay, C., Shi, M., Lo, N., Wille, M., Eden, J., Holmes, E. (2019). Novel hepatitis D-like agents in vertebrates and invertebrates. Virus Evolution, 5(2), 1-10. [More Information]
Charon, J., Grigg, M., Eden, J., Piera, K., Rana, H., William, T., Rose, K., Davenport, M., Anstey, N., Holmes, E. (2019). Novel RNA viruses associated with Plasmodium vivax in human malaria and Leucocytozoon parasites in avian disease. PLoS Pathogens, 15(12), 1-26. [More Information]
Kerr, P., Eden, J., Di Giallonardo, F., Peacock, D., Liu, J., Strive, T., Read, A., Holmes, E. (2019). Punctuated Evolution of Myxoma Virus: Rapid and Disjunct Evolution of a Recent Viral Lineage in Australia. Journal of Virology, 93(8), 1-18. [More Information]
Cobbin, J., Britton, P., Burrell, R., Thosar, D., Selvakumar, K., Eden, J., Jones, C., Holmes, E. (2018). A complex mosaic of enteroviruses shapes community-acquired hand, foot and mouth disease transmission and evolution within a single hospital. Virus Evolution, 4(2), 1-11. [More Information]
Wille, M., Netter, H., Littlejohn, M., Yuen, L., Shi, M., Eden, J., Klaassen, M., Holmes, E., Hurt, A. (2018). A Divergent Hepatitis D-Like Agent in Birds. Viruses, 10(12), 1-9. [More Information]
Hiener, B., Eden, J., Horsburgh, B., Palmer, S. (2018). Amplification of Near Full-length HIV-1 Proviruses for Next-Generation Sequencing. Journal of Visualized Experiments, 140, 1-12. [More Information]
Qi, W., Jia, W., Liu, D., Li, J., Bi, Y., Xie, S., Li, B., Hu, T., Du, Y., Eden, J., Holmes, E., et al (2018). Emergence and Adaptation of a Novel Highly Pathogenic H7N9 Influenza Virus in Birds and Humans from a 2013 Human-Infecting Low-Pathogenic Ancestor. Journal of Virology, 92(2), 1-12. [More Information]
Lun, J., Hewitt, J., Sitabkhan, A., Eden, J., Enosi, T., Netzler, N., Morrell, L., Merif, J., Jones, R., Huang, B., Dwyer, D., Kok, J., et al (2018). Emerging recombinant noroviruses identified by clinical and waste water screening. Emerging Microbes and Infections, 7(1), 1-14. [More Information]
Di Giallonardo, F., Kok, J., Fernandez, M., Carter, I., Geoghegan, J., Dwyer, D., Holmes, E., Eden, J. (2018). Evolution of human respiratory syncytial virus (RSV) over multiple seasons in New South Wales, Australia. Viruses, 10(9), 1-13. [More Information]
Shi, M., White, V., Schlub, T., Eden, J., Hoffman, A., Holmes, E. (2018). No detectable effect of Wolbachia wMel on the prevalence and abundance of the RNA virome of Drosophila melanogaster. Proceedings of the Royal Society B: Biological Sciences, 285(1883), 1-10. [More Information]
Shi, M., Lin, X., Chen, X., Tian, J., Chen, L., Li, K., Wang, W., Eden, J., Shen, J., Liu, L., Holmes, E., et al (2018). The evolutionary history of vertebrate RNA viruses. Nature, 556, 197-202. [More Information]
Patterson Ross, Z., Klunk, J., Fornaciari, G., Giuffra, V., Duchene, S., Duggan, A., Poinar, D., Douglas, M., Eden, J., Holmes, E., et al (2018). The paradox of HBV evolution as revealed from a 16th century mummy. PLoS Pathogens, 14(1), 1-25. [More Information]
Pollett, S., Trovao, N., Yi, T., Eden, J., Halpin, R., Bera, J., Das, S., Wentworth, D., Ocana, V., Mendocilla, S., et al (2018). The transmission dynamics and diversity of human metapneumovirus in Peru. Influenza and Other Respiratory Viruses, 12(4), 508-513. [More Information]
Russo, A., Eden, J., Tuipulotu, D., Shi, M., Selechnik, D., Shine, R., Rollins, L., Holmes, E., White, P. (2018). Viral discovery in the invasive Australian cane toad (Rhinella marina) using metatranscriptomic and genomic approaches. Journal of Virology, 92(17), 1-18. [More Information]
Geoghegan, J., Pirotta, V., Harvey, E., Smith, A., Buchmann, J., Ostrowski, M., Eden, J., Harcourt, R., Holmes, E. (2018). Virological Sampling of Inaccessible Wildlife with Drones. Viruses, 10(300), 1-7. [More Information]
Wille, M., Eden, J., Shi, M., Klaassen, M., Hurt, A., Holmes, E. (2018). Virus–virus interactions and host ecology are associated with RNA virome structure in wild birds. Molecular Ecology, 27(24), 5263-5278. [More Information]
Rose, K., Agius, J., Hall, J., Thompson, P., Eden, J., Srivastava, M., Tiernan, B., Jenkins, C., Phalen, D. (2017). Emergent multisystemic Enterococcus infection threatens endangered Christmas Island reptile populations. PloS One, 12(7), 1-21. [More Information]
Eden, J., Rose, K., Ng, J., Shi, M., Wang, Q., Sintchenko, V., Holmes, E. (2017). Francisella tularensis subsp. holarctica in Ringtail Possums, Australia. Emerging Infectious Diseases, 23(7), 1198-1201. [More Information]
Kerr, P., Cattadori, I., Rogers, M., Fitch, A., Geber, A., Liu, J., Sim, D., Boag, B., Eden, J., Ghedin, E., Holmes, E., et al (2017). Genomic and phenotypic characterization of myxoma virus from Great Britain reveals multiple evolutionary pathways distinct from those in Australia. PLoS Pathogens, 13(3), e1006252. [More Information]
Shi, M., Neville, P., Nicholson, J., Eden, J., Imrie, A., Holmes, E. (2017). High-Resolution Metatranscriptomics Reveals the Ecological Dynamics of Mosquito-Associated RNA Viruses in Western Australia. Journal of Virology, 91(17), e00680-17. [More Information]
Hiener, B., Horsburgh, B., Eden, J., Barton, K., Schlub, T., Lee, E., van Stockenstrom, S., Odevall, L., Milush, J., Liegler, T., Palmer, S., et al (2017). Identification of Genetically Intact HIV-1 Proviruses in Specific CD4+ T Cells from Effectively Treated Participants. Cell Reports, 21(3), 813-822. [More Information]
Eden, J., Chisholm, R., Bull, R., White, P., Holmes, E., Tanaka, M. (2017). Persistent infections in immunocompromised hosts are rarely sources of new pathogen variants. Virus Evolution, 3(2), vex018. [More Information]
Le Pendu, J., Abrantes, J., Bertagnoli, S., Guitton, J., Le Gall-Recule, G., Lopes, A., Marchandeau, S., Alda, F., Almeida, T., Celio, A., Eden, J., Mahar, J., et al (2017). Proposal for a unified classification system and nomenclature of lagoviruses. Journal of General Virology, 98(7), 1658-1666. [More Information]
Liu, J., Cattadori, I., Sim, D., Eden, J., Holmes, E., Read, A., Kerr, P. (2017). Reverse engineering field isolates of myxoma virus demonstrates that some gene disruptions or losses of function do not explain virulence changes observed in the field. Journal of Virology, 91(20), 1-18. [More Information]
Lim, K., Hewitt, J., Sitabkhan, A., Eden, J., Lun, J., Levy, A., Merif, J., Smith, D., Rawlinson, W., White, P. (2016). A Multi-Site Study of Norovirus Molecular Epidemiology in Australia and New Zealand, 2013-2014. PloS One, 11(4), 1-19. [More Information]
Mahar, J., Nicholson, L., Eden, J., Duchene, S., Kerr, P., Duckworth, J., Ward, V., Holmes, E., Strive, T. (2016). Benign Rabbit Caliciviruses Exhibit Evolutionary Dynamics Similar to Those of Their Virulent Relatives. Journal of Virology, 90(20), 9317-9329. [More Information]
Duchene, S., Duchene, D., Di Giallonardo, F., Eden, J., Geoghegan, J., Holt, K., Ho, S., Holmes, E. (2016). Cross-validation to select Bayesian hierarchical models in phylogenetics. BMC Evolutionary Biology, 16(1), 1-8. [More Information]
Shi, M., Lin, X., Tian, J., Chen, L., Chen, X., Li, C., Qin, X., Li, J., Cao, J., Eden, J., Buchmann, J., Holmes, E., et al (2016). Redefining the invertebrate RNA virosphere. Nature, 540(7634), 539-543. [More Information]
Eden, J., Kovaliski, J., Duckworth, J., Swain, G., Maher, J., Strive, T., Holmes, E. (2015). Comparative phylodynamics of rabbit hemorrhagic disease virus in Australia and New Zealand. Journal of Virology, 89(18), 9548-9558. [More Information]
Alhammad, Y., Maharajh, S., Butcher, R., Eden, J., White, P., Poumbourios, P., Drummer, H. (2015). Longitudinal sequence and functional evolution within glycoprotein E2 in hepatitis C virus genotype 3a infection. PloS One, 10(5), 1-19. [More Information]
Eden, J., Read, A., Duckworth, J., Strive, T., Holmes, E. (2015). Resolving the Origin of Rabbit Hemorrhagic Disease Virus: Insights from an Investigation of the Viral Stocks Released in Australia. Journal of Virology, 89(23), 12217-12220. [More Information]
Eltahla, A., Lim, K., Eden, J., Kelly, A., Mackenzie, J., White, P. (2014). Nonnucleoside Inhibitors of Norovirus RNA Polymerase: Scaffolds for Rational Drug Design. Antimicrobial Agents and Chemotherapy, 58(6), 3115-3123. [More Information]
Eden, J., Hewitt, J., Lim, K., Boni, M., Merif, J., Greening, G., Ratcliff, R., Holmes, E., Tanaka, M., Rawlinson, W., et al (2014). The emergence and evolution of the novel epidemic norovirus GII.4 variant Sydney 2012. Virology, 450-451, 106-113. [More Information]
Eltahla, A., Lackovic, K., Marquis, C., Eden, J., White, P. (2013). A fluorescence-based high-throughput screen to identify small compound inhibitors of the genotype 3a hepatitis c virus RNA polymerase. Journal of Biomolecular Screening, 18(9), 1027-1034. [More Information]
Cui, J., Eden, J., Holmes, E., Wang, L. (2013). Adaptive evolution of bat dipeptidyl peptidase 4 (dpp4): Implications for the origin and emergence of Middle East Respiratory Syndrome Coronavirus. Virology Journal, 10, 1-5. [More Information]
van Beek, J., Ambert-Balay, K., Botteldoorn, N., Eden, J., Fonager, J., Hewitt, J., Iritani, N., Kroneman, A., Vennema, H., Vinjé, J., et al (2013). Indications for worldwide increased norovirus activity associated with emergence of a new variant of Genotype II.4, LATE 2012. Eurosurveillance, 18(1).
Eden, J., Kun, L., Lynette, L., White, P. (2013). Molecular epidemiology of norovirus in Singapore, 2004-2011. Journal of Medical Virology, 85(10), 1842-1851. [More Information]
Eden, J., Tanaka, M., Boni, M., Rawlinson, W., White, P. (2013). Recombination within the pandemic norovirus GII.4 lineage. Journal of Virology, 87(11), 6270-6282. [More Information]
Eden, J., Lim, K., White, P. (2012). Complete genome of the human norovirus GIV.1 strain Lake Macquarie virus. Journal of Virology, 86(18), 10251-10252. [More Information]
Bull, R., Eden, J., Luciani, F., McElroy, K., Rawlinson, W., White, P. (2012). Contribution of intra- and interhost dynamics to norovirus evolution. Journal of Virology, 86(6), 3219-3229. [More Information]
White, P., Eden, J., Hansman, G. (2012). Molecular epidemiology of noroviruses and sapoviruses and their role in Australian outbreaks of acute gastroenteritis. Microbiology Australia, 33(2), 70-73.
Eden, J., Sharpe, L., White, P., Brown, A. (2011). Norovirus RNA-dependent RNA polymerase is phosphorylated by an important survival kinase, Akt. Journal of Virology, 85(20), 10894-10898. [More Information]
Eden, J., Bull, R., Tu, E., McIver, C., Lyon, M., Marshall, J., Smith, D., Musto, J., Rawlinson, W., White, P. (2010). Norovirus GII.4 variant 2006b caused epidemics of acute gastroenteritis in Australia during 2007 and 2008. Journal Of Clinical Virology, 49(4), 265-271. [More Information]
Bull, R., Eden, J., Rawlinson, W., White, P. (2010). Rapid evolution of pandemic noroviruses of the GII.4 lineage. PLoS Pathogens, 6(3), e1000831. [More Information]

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Conferences

Eden, J., Lim, K., Ballouk, R., Rawlinson, W., Tanaka, M., White, P. (2012). Complex patterns of evolution led to the emergence of the current norovirus pandemic GII.4 variant, termed New Orleans 2010. 2012 Asia-Pacific Congress of Medical Virology, Adelaide, South Australia, Australia.
Eden, J., Bull, R., White, P. (2011). Evidence of intra-genotype recombination in the evolution of a novel norovirus GII.4 variant associated with outbreaks in NSW, Australia during 2009. Australian Microbiology Society Annual Scientific Meeting.
Eden, J., Bull, R., White, P. (2010). Evolution of a novel GII.4 associated with outbreaks of gastroenteritis in NSW, Australia during 2009. International Calicivirus Conference.
Eden, J., Bull, R., Tu, E., Lim, H., McIver, C., Lyon, M., Marshall, J., Smith, D., Musto, J., Rawlinson, W., et al (2009). Norovirus GII.4 variant, 2006b, continues to cause gastroenteritis epidemics across Australia in 2007 and 2008. Australian Virology Group Meeting.

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2023

Hurley, S., McMullan, B., Williams, D., Watson, J., Solinas, A., Kim, K., Rawlinson, W., Eden, J., Bingham, J., Rodriguez, M., Howard-Jones, A., et al (2023). Fatal Human Neurologic Infection Caused by Pigeon Avian Paramyxovirus-1, Australia. Emerging Infectious Diseases, 29(12), 2482-2487. [More Information]
Maamary, J., Maddocks, S., Barnett, Y., Wong, S., Rodriguez, M., Hueston, L., Jeoffreys, N., Eden, J., Dwyer, D., Floyd, T., et al (2023). New Detection of Locally Acquired Japanese Encephalitis Virus Using Clinical Metagenomics, New South Wales, Australia. Emerging Infectious Diseases, 29(3), 627-630. [More Information]

2022

Horsburgh, B., Hiener, B., Fisher, K., Lee, E., Morgan, H., Eden, J., von Stockenstrom, S., Odevall, L., Milush, J., Hoh, R., Schlub, T., Palmer, S., et al (2022). Cellular Activation, Differentiation, and Proliferation Influence the Dynamics of Genetically Intact Proviruses over Time. The Journal of Infectious Diseases, 225(7), 1168-1178. [More Information]
Pham, D., Howard-Jones, A., Hueston, L., Jeoffreys, N., Doggett, S., Rockett, R., Eden, J., Sintchenko, V., Chen, S., O'Sullivan, M., Dwyer, D., et al (2022). Emergence of Japanese encephalitis in Australia: a diagnostic perspective. Pathology, 54(6), 669-677. [More Information]
Howard-Jones, A., Pham, D., Jeoffreys, N., Eden, J., Hueston, L., Kesson, A., Nagendra, V., Samarasekara, H., Newton, P., Chen, S., O'Sullivan, M., Dwyer, D., Kok, J., et al (2022). Emerging Genotype IV Japanese Encephalitis Virus Outbreak in New South Wales, Australia. Viruses, 14(9). [More Information]
Cole, B., Lambrechts, L., Boyer, Z., Noppe, Y., De Scheerder, M., Eden, J., Vrancken, B., Schlub, T., McLaughlin, S., Frenkel, L., Palmer, S., et al (2022). Extensive characterization of HIV-1 reservoirs reveals links to plasma viremia before and during analytical treatment interruption. Cell Reports, 39(4), 110739. [More Information]
Peel, A., Yinda, C., Annand, E., Dale, A., Eby, P., Eden, J., Jones, D., Kessler, M., Lunn, T., Schulz, J., et al (2022). Novel Hendra Virus Variant Circulating in Black Flying Foxes and Grey-Headed Flying Foxes, Australia. Emerging Infectious Diseases, 28(5), 1043-1047. [More Information]
Taylor, J., Thompson, K., Annand, E., Massey, P., Bennett, J., Eden, J., Horsburgh, B., Hodgson, E., Wood, K., Kerr, J., et al (2022). Novel variant Hendra virus genotype 2 infection in a horse in the greater Newcastle region, New South Wales, Australia. One Health, 15, Article number 100423-1-Article number 100423-7. [More Information]
Eden, J., Sikazwe, C., Xie, R., Deng, Y., Sullivan, S., Michie, A., Levy, A., Cutmore, E., Blyth, C., Britton, P., Dwyer, D., Horsburgh, B., Tulloch, R., Holmes, E., et al (2022). Off-season RSV epidemics in Australia after easing of COVID-19 restrictions. Nature Communications, 13(2884). [More Information]
Fisher, K., Wang, X., Lee, A., Morcilla, V., De Vries, A., Lee, E., Eden, J., Deeks, S., Kelleher, A., Palmer, S. (2022). Plasma-Derived HIV-1 Virions Contain Considerable Levels of Defective Genomes. Journal of Virology, 96(6), e0201121. [More Information]

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2021

Tulloch, R., Kok, J., Carter, I., Dwyer, D., Eden, J. (2021). An amplicon-based approach for the whole-genome sequencing of human metapneumovirus. Viruses, 13(3), 499-1-499-11. [More Information]
Eden, J. (2021). Genome sequencing and its use in public health responses to COVID-19. Microbiology Australia, 42(1), 44-46. [More Information]
Agius, J., Phalen, D., Rose, K., Eden, J. (2021). Genomic Insights Into the Pathogenicity of a Novel Biofilm-Forming Enterococcus sp. Bacteria (Enterococcus lacertideformus) Identified in Reptiles. Frontiers in Microbiology, 12, 635208. [More Information]
Lee, E., Sandgren, K., Duette, G., Stylianou, V., Khanna, R., Eden, J., Blyth, E., Gottlieb, D., Cunningham, A., Palmera, S. (2021). Identification of SARS-CoV-2 nucleocapsid and spike T-cell epitopes for assessing T-cell immunity. Journal of Virology, 95(6), 2002. [More Information]
Porter, A., Cobbin, J., Li, C., Eden, J., Holmes, E. (2021). Metagenomic identification of viral sequences in laboratory reagents. Viruses, 13(11), 2122. [More Information]
Robertson, M., Eden, J., Levy, A., Carter, I., Tulloch, R., Cutmore, E., Horsburgh, B., Sikazwe, C., Dwyer, D., Smith, D., et al (2021). The spatial-temporal dynamics of respiratory syncytial virus infections across the east–west coasts of Australia during 2016–17. Virus Evolution, 7(2), A1360. [More Information]

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2020

Ortiz-Baez, A., Eden, J., Moritz, C., Holmes, E. (2020). A Divergent Articulavirus in an Australian Gecko Identified Using Meta-Transcriptomics and Protein Structure Comparisons. Viruses, 12(6), 613. [More Information]
Eden, J., Rockett, R., Carter, I., Rahman, H., de Ligt, J., Hadfield, J., Storey, M., Ren, X., Tulloch, R., Basile, K., Sintchenko, V., Chen, S., Sorrell, T., Holmes, E., Dwyer, D., et al (2020). An emergent clade of SARS-CoV-2 linked to returned travellers from Iran. Virus Evolution, 6(1), veaa027. [More Information]
Bull, R., Adikari, T., Ferguson, J., Hammond, J., Stevanovski, I., Beukers, A., Naing, Z., Yeang, M., Verich, A., Gamaarachchi, H., Eden, J., Van Hal, S., et al (2020). Analytical validity of nanopore sequencing for rapid SARS-CoV-2 genome analysis. Nature Communications, 11(1), 1-8. [More Information]
Nguyen, T., Pham, T., Van, T., Nguyen, T., Ngoc Nguyen, D., Minh Le, H., Eden, J., Rockett, R., Hong Nguyen, T., Ngoc Vu, B., Dwyer, D., et al (2020). Genetic diversity of SARS-CoV-2 and clinical, epidemiological characteristics of COVID-19 patients in Hanoi, Vietnam. PloS One, 15, 1-15. [More Information]
Horsburgh, B., Lee, E., Hiener, B., Eden, J., Schlub, T., von Stockenstrom, S., Odevall, L., Milush, J., Liegler, T., Sinclair, E., Palmer, S., et al (2020). High levels of genetically intact HIV in HLA-DR+ memory T cells indicates their value for reservoir studies. AIDS, 34(5), 659-668. [More Information]
Tuddenham, R., Eden, J., Gilbey, T., Dwyer, D., Jennings, Z., Holmes, E., Branley, J. (2020). Human pegivirus in brain tissue of a patient with encephalitis. Diagnostic Microbiology and Infectious Disease, 96(2), 1-3. [More Information]
Rahman, H., Carter, I., Basile, K., Donovan, L., Kumar, S., Tran, T., Ko, D., Alderson, S., Sivaruban, T., Eden, J., O'Sullivan, M., Sintchenko, V., Chen, S., Dwyer, D., et al (2020). Interpret with caution: An evaluation of the commercial AusDiagnostics versus in-house developed assays for the detection of SARS-CoV-2 virus. Journal Of Clinical Virology, 127, 1-6. [More Information]
Ortiz-Baez, A., Cousins, K., Eden, J., Chang, W., Harvey, E., Pettersson, J., Carver, S., Polkinghorne, A., Slapeta, J., Rose, K., Holmes, E. (2020). Meta‑transcriptomic identification of Trypanosoma spp. in native wildlife species from Australia. Parasites and Vectors, 13(477), 1-10. [More Information]
Chang, W., Eden, J., Hall, J., Shi, M., Rose, K., Holmes, E. (2020). Meta-transcriptomic analysis of virus diversity in urban wild birds with paretic disease. Journal of Virology, 94(18), 1-22. [More Information]
Chang, W., Li, C., Hall, J., Eden, J., Hyndman, T., Holmes, E., Rose, K. (2020). Meta-transcriptomic discovery of a divergent circovirus and a chaphamaparvovirus in captive reptiles with proliferative respiratory syndrome. Viruses, 12(10), 1073. [More Information]
Turnbull, O., Ortiz-Baez, A., Eden, J., Shi, M., Williamson, J., Gaston, T., Zhang, Y., Holmes, E., Geohegan, J. (2020). Meta-Transcriptomic Identification of Divergent Amnoonviridae in Fish. Viruses, 12(11), 1-10. [More Information]
Porter, A., Pettersson, J., Chang, W., Harvey, E., Rose, K., Shi, M., Eden, J., Buchmann, J., Moritz, C., Holmes, E. (2020). Novel hepaci- and pegi-like viruses in native Australian wildlife and non-human primates. Virus Evolution, 6(2), 1-13. [More Information]
Vaz, F., Raso, T., Agius, J., Hunt, T., Leishman, A., Eden, J., Phalen, D. (2020). Opportunistic sampling of wild native and invasive birds reveals a rich diversity of adenoviruses in Australia. Virus Evolution, 6(1), 1-13. [More Information]
Basile, K., Habibur Rahman, H., Carter, I., Donovan, L., Kumar, S., Tran, T., Ko, D., Alderson, S., Sivaruban, T., Eden, J., Rockett, R., O'Sullivan, M., Sintchenko, V., Chen, S., Maddocks, S., Dwyer, D., Kok, J. (2020). Response. Journal Of Clinical Virology, 130, e19779. [More Information]
Rockett, R., Arnott, A., Lam, C., Sadsad, R., Timms, V., Gray, K., Eden, J., Chang, S., Gall, M., Draper, J., O'Sullivan, M., Chen, S., Sorrell, T., Dwyer, D., Holmes, E., Kok, J., Prokopenko, M., Sintchenko, V., et al (2020). Revealing COVID-19 transmission in Australia by SARS-CoV-2 genome sequencing and agent-based modeling. Nature Medicine, 26(9), 1398-1404. [More Information]

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2019

Phalen, D., Agius, J., Vaz, F., Eden, J., Setyo, L., Donahoe, S. (2019). A survey of a mixed species aviary provides new insights into the pathogenicity, diversity, evolution, host range, and distribution of psittacine and passerine adenoviruses. Avian pathology, 48(5), 437-443. [More Information]
Porter, A., Shi, M., Eden, J., Zhang, Y., Holmes, E. (2019). Diversity and Evolution of Novel Invertebrate DNA Viruses Revealed by Meta-Transcriptomics. Viruses, 11, 1-21. [More Information]
Harvey, E., Rose, K., Eden, J., Lo, N., Abeyasuriya, T., Shi, M., Doggett, S., Holmes, E. (2019). Extensive Diversity of RNA Viruses in Australian Ticks. Journal of Virology, 93(3), 1-15. [More Information]
Douglas, M., Tay, E., Eden, J., George, J. (2019). Hepatitis C Virus Genotype 8 - successful treatment with sofosbuvir/velpatasvir. The Journal of Infectious Diseases, 220(4), 720-722. [More Information]
Harvey, E., Rose, K., Eden, J., Lawrence, A., Doggett, S., Holmes, E. (2019). Identification of diverse arthropod associated viruses in native Australian fleas. Virology, 535, 189-199. [More Information]
Pettersson, J., Shi, M., Eden, J., Holmes, E., Hesson, J. (2019). Meta-transcriptomic comparison of the RNA Viromes of the mosquito vectors culex pipiens and culex torrentium in Northern Europe. Viruses, 11, 1-20. [More Information]
Marcelino, V., Wille, M., Hurt, A., Gonzalez-Acuna, D., Klaassen, M., Schlub, T., Eden, J., Shi, M., Iredell, J., Sorrell, T., Holmes, E. (2019). Meta-transcriptomics reveals a diverse antibiotic resistance gene pool in avian microbiomes. BMC Biology, 17(1), 1-11. [More Information]
Marcelino, V., Irinyi, L., Eden, J., Meyer, W., Holmes, E., Sorrell, T. (2019). Metatranscriptomics as a tool to identify fungal species and subspecies in mixed communities – a proof of concept under laboratory conditions. IMA Fungus, 10(1), 1-10. [More Information]
Agius, J., Phalen, D., Rose, K., Eden, J. (2019). New insights into Sauropsid Papillomaviridae evolution and epizootiology: discovery of two novel papillomaviruses in native and invasive Island geckos. Virus Evolution, 5(2), 1-12. [More Information]
Chang, W., Pettersson, J., Le Lay, C., Shi, M., Lo, N., Wille, M., Eden, J., Holmes, E. (2019). Novel hepatitis D-like agents in vertebrates and invertebrates. Virus Evolution, 5(2), 1-10. [More Information]
Charon, J., Grigg, M., Eden, J., Piera, K., Rana, H., William, T., Rose, K., Davenport, M., Anstey, N., Holmes, E. (2019). Novel RNA viruses associated with Plasmodium vivax in human malaria and Leucocytozoon parasites in avian disease. PLoS Pathogens, 15(12), 1-26. [More Information]
Kerr, P., Eden, J., Di Giallonardo, F., Peacock, D., Liu, J., Strive, T., Read, A., Holmes, E. (2019). Punctuated Evolution of Myxoma Virus: Rapid and Disjunct Evolution of a Recent Viral Lineage in Australia. Journal of Virology, 93(8), 1-18. [More Information]

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2018

Cobbin, J., Britton, P., Burrell, R., Thosar, D., Selvakumar, K., Eden, J., Jones, C., Holmes, E. (2018). A complex mosaic of enteroviruses shapes community-acquired hand, foot and mouth disease transmission and evolution within a single hospital. Virus Evolution, 4(2), 1-11. [More Information]
Wille, M., Netter, H., Littlejohn, M., Yuen, L., Shi, M., Eden, J., Klaassen, M., Holmes, E., Hurt, A. (2018). A Divergent Hepatitis D-Like Agent in Birds. Viruses, 10(12), 1-9. [More Information]
Hiener, B., Eden, J., Horsburgh, B., Palmer, S. (2018). Amplification of Near Full-length HIV-1 Proviruses for Next-Generation Sequencing. Journal of Visualized Experiments, 140, 1-12. [More Information]
Qi, W., Jia, W., Liu, D., Li, J., Bi, Y., Xie, S., Li, B., Hu, T., Du, Y., Eden, J., Holmes, E., et al (2018). Emergence and Adaptation of a Novel Highly Pathogenic H7N9 Influenza Virus in Birds and Humans from a 2013 Human-Infecting Low-Pathogenic Ancestor. Journal of Virology, 92(2), 1-12. [More Information]
Lun, J., Hewitt, J., Sitabkhan, A., Eden, J., Enosi, T., Netzler, N., Morrell, L., Merif, J., Jones, R., Huang, B., Dwyer, D., Kok, J., et al (2018). Emerging recombinant noroviruses identified by clinical and waste water screening. Emerging Microbes and Infections, 7(1), 1-14. [More Information]
Di Giallonardo, F., Kok, J., Fernandez, M., Carter, I., Geoghegan, J., Dwyer, D., Holmes, E., Eden, J. (2018). Evolution of human respiratory syncytial virus (RSV) over multiple seasons in New South Wales, Australia. Viruses, 10(9), 1-13. [More Information]
Shi, M., White, V., Schlub, T., Eden, J., Hoffman, A., Holmes, E. (2018). No detectable effect of Wolbachia wMel on the prevalence and abundance of the RNA virome of Drosophila melanogaster. Proceedings of the Royal Society B: Biological Sciences, 285(1883), 1-10. [More Information]
Shi, M., Lin, X., Chen, X., Tian, J., Chen, L., Li, K., Wang, W., Eden, J., Shen, J., Liu, L., Holmes, E., et al (2018). The evolutionary history of vertebrate RNA viruses. Nature, 556, 197-202. [More Information]
Patterson Ross, Z., Klunk, J., Fornaciari, G., Giuffra, V., Duchene, S., Duggan, A., Poinar, D., Douglas, M., Eden, J., Holmes, E., et al (2018). The paradox of HBV evolution as revealed from a 16th century mummy. PLoS Pathogens, 14(1), 1-25. [More Information]
Pollett, S., Trovao, N., Yi, T., Eden, J., Halpin, R., Bera, J., Das, S., Wentworth, D., Ocana, V., Mendocilla, S., et al (2018). The transmission dynamics and diversity of human metapneumovirus in Peru. Influenza and Other Respiratory Viruses, 12(4), 508-513. [More Information]
Russo, A., Eden, J., Tuipulotu, D., Shi, M., Selechnik, D., Shine, R., Rollins, L., Holmes, E., White, P. (2018). Viral discovery in the invasive Australian cane toad (Rhinella marina) using metatranscriptomic and genomic approaches. Journal of Virology, 92(17), 1-18. [More Information]
Geoghegan, J., Pirotta, V., Harvey, E., Smith, A., Buchmann, J., Ostrowski, M., Eden, J., Harcourt, R., Holmes, E. (2018). Virological Sampling of Inaccessible Wildlife with Drones. Viruses, 10(300), 1-7. [More Information]
Wille, M., Eden, J., Shi, M., Klaassen, M., Hurt, A., Holmes, E. (2018). Virus–virus interactions and host ecology are associated with RNA virome structure in wild birds. Molecular Ecology, 27(24), 5263-5278. [More Information]

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2017

Rose, K., Agius, J., Hall, J., Thompson, P., Eden, J., Srivastava, M., Tiernan, B., Jenkins, C., Phalen, D. (2017). Emergent multisystemic Enterococcus infection threatens endangered Christmas Island reptile populations. PloS One, 12(7), 1-21. [More Information]
Eden, J., Rose, K., Ng, J., Shi, M., Wang, Q., Sintchenko, V., Holmes, E. (2017). Francisella tularensis subsp. holarctica in Ringtail Possums, Australia. Emerging Infectious Diseases, 23(7), 1198-1201. [More Information]
Kerr, P., Cattadori, I., Rogers, M., Fitch, A., Geber, A., Liu, J., Sim, D., Boag, B., Eden, J., Ghedin, E., Holmes, E., et al (2017). Genomic and phenotypic characterization of myxoma virus from Great Britain reveals multiple evolutionary pathways distinct from those in Australia. PLoS Pathogens, 13(3), e1006252. [More Information]
Shi, M., Neville, P., Nicholson, J., Eden, J., Imrie, A., Holmes, E. (2017). High-Resolution Metatranscriptomics Reveals the Ecological Dynamics of Mosquito-Associated RNA Viruses in Western Australia. Journal of Virology, 91(17), e00680-17. [More Information]
Hiener, B., Horsburgh, B., Eden, J., Barton, K., Schlub, T., Lee, E., van Stockenstrom, S., Odevall, L., Milush, J., Liegler, T., Palmer, S., et al (2017). Identification of Genetically Intact HIV-1 Proviruses in Specific CD4+ T Cells from Effectively Treated Participants. Cell Reports, 21(3), 813-822. [More Information]
Eden, J., Chisholm, R., Bull, R., White, P., Holmes, E., Tanaka, M. (2017). Persistent infections in immunocompromised hosts are rarely sources of new pathogen variants. Virus Evolution, 3(2), vex018. [More Information]
Le Pendu, J., Abrantes, J., Bertagnoli, S., Guitton, J., Le Gall-Recule, G., Lopes, A., Marchandeau, S., Alda, F., Almeida, T., Celio, A., Eden, J., Mahar, J., et al (2017). Proposal for a unified classification system and nomenclature of lagoviruses. Journal of General Virology, 98(7), 1658-1666. [More Information]
Liu, J., Cattadori, I., Sim, D., Eden, J., Holmes, E., Read, A., Kerr, P. (2017). Reverse engineering field isolates of myxoma virus demonstrates that some gene disruptions or losses of function do not explain virulence changes observed in the field. Journal of Virology, 91(20), 1-18. [More Information]

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2016

Lim, K., Hewitt, J., Sitabkhan, A., Eden, J., Lun, J., Levy, A., Merif, J., Smith, D., Rawlinson, W., White, P. (2016). A Multi-Site Study of Norovirus Molecular Epidemiology in Australia and New Zealand, 2013-2014. PloS One, 11(4), 1-19. [More Information]
Mahar, J., Nicholson, L., Eden, J., Duchene, S., Kerr, P., Duckworth, J., Ward, V., Holmes, E., Strive, T. (2016). Benign Rabbit Caliciviruses Exhibit Evolutionary Dynamics Similar to Those of Their Virulent Relatives. Journal of Virology, 90(20), 9317-9329. [More Information]
Duchene, S., Duchene, D., Di Giallonardo, F., Eden, J., Geoghegan, J., Holt, K., Ho, S., Holmes, E. (2016). Cross-validation to select Bayesian hierarchical models in phylogenetics. BMC Evolutionary Biology, 16(1), 1-8. [More Information]
Shi, M., Lin, X., Tian, J., Chen, L., Chen, X., Li, C., Qin, X., Li, J., Cao, J., Eden, J., Buchmann, J., Holmes, E., et al (2016). Redefining the invertebrate RNA virosphere. Nature, 540(7634), 539-543. [More Information]

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2015

Eden, J., Kovaliski, J., Duckworth, J., Swain, G., Maher, J., Strive, T., Holmes, E. (2015). Comparative phylodynamics of rabbit hemorrhagic disease virus in Australia and New Zealand. Journal of Virology, 89(18), 9548-9558. [More Information]
Alhammad, Y., Maharajh, S., Butcher, R., Eden, J., White, P., Poumbourios, P., Drummer, H. (2015). Longitudinal sequence and functional evolution within glycoprotein E2 in hepatitis C virus genotype 3a infection. PloS One, 10(5), 1-19. [More Information]
Eden, J., Read, A., Duckworth, J., Strive, T., Holmes, E. (2015). Resolving the Origin of Rabbit Hemorrhagic Disease Virus: Insights from an Investigation of the Viral Stocks Released in Australia. Journal of Virology, 89(23), 12217-12220. [More Information]

2014

Eltahla, A., Lim, K., Eden, J., Kelly, A., Mackenzie, J., White, P. (2014). Nonnucleoside Inhibitors of Norovirus RNA Polymerase: Scaffolds for Rational Drug Design. Antimicrobial Agents and Chemotherapy, 58(6), 3115-3123. [More Information]
Eden, J., Hewitt, J., Lim, K., Boni, M., Merif, J., Greening, G., Ratcliff, R., Holmes, E., Tanaka, M., Rawlinson, W., et al (2014). The emergence and evolution of the novel epidemic norovirus GII.4 variant Sydney 2012. Virology, 450-451, 106-113. [More Information]

2013

Eltahla, A., Lackovic, K., Marquis, C., Eden, J., White, P. (2013). A fluorescence-based high-throughput screen to identify small compound inhibitors of the genotype 3a hepatitis c virus RNA polymerase. Journal of Biomolecular Screening, 18(9), 1027-1034. [More Information]
Cui, J., Eden, J., Holmes, E., Wang, L. (2013). Adaptive evolution of bat dipeptidyl peptidase 4 (dpp4): Implications for the origin and emergence of Middle East Respiratory Syndrome Coronavirus. Virology Journal, 10, 1-5. [More Information]
van Beek, J., Ambert-Balay, K., Botteldoorn, N., Eden, J., Fonager, J., Hewitt, J., Iritani, N., Kroneman, A., Vennema, H., Vinjé, J., et al (2013). Indications for worldwide increased norovirus activity associated with emergence of a new variant of Genotype II.4, LATE 2012. Eurosurveillance, 18(1).
Eden, J., Kun, L., Lynette, L., White, P. (2013). Molecular epidemiology of norovirus in Singapore, 2004-2011. Journal of Medical Virology, 85(10), 1842-1851. [More Information]
Eden, J., Tanaka, M., Boni, M., Rawlinson, W., White, P. (2013). Recombination within the pandemic norovirus GII.4 lineage. Journal of Virology, 87(11), 6270-6282. [More Information]

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2012

Eden, J., Lim, K., White, P. (2012). Complete genome of the human norovirus GIV.1 strain Lake Macquarie virus. Journal of Virology, 86(18), 10251-10252. [More Information]
Eden, J., Lim, K., Ballouk, R., Rawlinson, W., Tanaka, M., White, P. (2012). Complex patterns of evolution led to the emergence of the current norovirus pandemic GII.4 variant, termed New Orleans 2010. 2012 Asia-Pacific Congress of Medical Virology, Adelaide, South Australia, Australia.
Bull, R., Eden, J., Luciani, F., McElroy, K., Rawlinson, W., White, P. (2012). Contribution of intra- and interhost dynamics to norovirus evolution. Journal of Virology, 86(6), 3219-3229. [More Information]
White, P., Eden, J., Hansman, G. (2012). Molecular epidemiology of noroviruses and sapoviruses and their role in Australian outbreaks of acute gastroenteritis. Microbiology Australia, 33(2), 70-73.

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2011

Eden, J., Bull, R., White, P. (2011). Evidence of intra-genotype recombination in the evolution of a novel norovirus GII.4 variant associated with outbreaks in NSW, Australia during 2009. Australian Microbiology Society Annual Scientific Meeting.
Eden, J., Sharpe, L., White, P., Brown, A. (2011). Norovirus RNA-dependent RNA polymerase is phosphorylated by an important survival kinase, Akt. Journal of Virology, 85(20), 10894-10898. [More Information]

2010

Eden, J., Bull, R., White, P. (2010). Evolution of a novel GII.4 associated with outbreaks of gastroenteritis in NSW, Australia during 2009. International Calicivirus Conference.
Eden, J., Bull, R., Tu, E., McIver, C., Lyon, M., Marshall, J., Smith, D., Musto, J., Rawlinson, W., White, P. (2010). Norovirus GII.4 variant 2006b caused epidemics of acute gastroenteritis in Australia during 2007 and 2008. Journal Of Clinical Virology, 49(4), 265-271. [More Information]
Bull, R., Eden, J., Rawlinson, W., White, P. (2010). Rapid evolution of pandemic noroviruses of the GII.4 lineage. PLoS Pathogens, 6(3), e1000831. [More Information]

2009

Eden, J., Bull, R., Tu, E., Lim, H., McIver, C., Lyon, M., Marshall, J., Smith, D., Musto, J., Rawlinson, W., et al (2009). Norovirus GII.4 variant, 2006b, continues to cause gastroenteritis epidemics across Australia in 2007 and 2008. Australian Virology Group Meeting.

Selected Grants

2025

Enhanced Viral Surveillance: A Capture Sequencing Panel for Emerging Bat Viruses, Peel A, Eden J, Sydney Institute for Infectious Diseases (Sydney ID)/Sydney ID Seed Grants
Unlocking Viral Persistence - Investigating Feral Pigs as Sentinels for Japanese Encephalitis Virus and Other Emerging Pathogens, Jenns K, Eden J, Sydney Institute for Infectious Diseases (Sydney ID)/Sydney ID Seed Grants

2022

Building active surveillance systems to track hepatitis C virusepidemiology and antiviral resistance, Douglas M, Kok J, Eden J, Tu T, Cunningham A, George J, Australian Centre for HIV and Hepatitis Virology Research (ACH2)/Research Support

2021

Meta-GP: Delivering a Clinical Metagenomics Platform for Australia, Dwyer D, Holmes E, Williamson D, Britton P, Sintchenko V, Eden J, Department of Health and Aged Care (Federal)/MRFF - Genomic Health Futures Mission (GHFM) - Project Grant

2020

BEAT COVID, Sorrell T, Ward R, Snelling T, Snelling T, Nicholson A, Grieve S, Macartney K, O'Sullivan M, Thevarajan I, Bull R, Britton P, Cunningham A, Eden J, Smith D, Imrie A, Tang B, Brilot-Turville F, Snow Medical Research Foundation Ltd/Pandemic Response Capacity Building

2018

Centre for Pathogen Discovery, Holmes E, Shi M, Eden J, Sintchenko V, Lo N, Barrs V, Beatty J, Hudson B, Rose K, Rockett R, DVC Research/Sydney Research Excellence Initiative 2020 (SREI)

2017

Centre for Pathogen Discovery, Holmes E, Sintchenko V, Lo N, Shi M, Eden J, Hudson B, DVC Research/Sydney Research Excellence Initiative 2020 (SREI)

2013

Integrating genotype and phenotype in clinical molecular epidemiology, Eden J, National Health and Medical Research Council (NHMRC)/Early Career Fellowships

In the media

COVID-19

Science meets business (link)

Hendra virus

USyd media release (link)
The Australian news article (link)

Tularemia in Ringtail Possums

USyd media release (link)
Conversation piece (link)
Xinhua news article (link)

Faculty of Medicine and Health

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Dr John-Sebastian Eden

Publications

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Selected Grants

2025

2022

2021

2020

2018

2017

2013

In the media