About Dr John-Sebastian Eden

Dr John-Sebastian Eden is a Research Scientist in Bioinformatics and Genomics based at the Westmead Institute for Medical Research and Senior Research Fellow in the Sydney Medical School. He is a Virologist and expert in Pathogen Genomics, who joined the University of Sydney in 2013 with a post-doctoral position in the research group of Professor Eddie Holmes and after he complete his PhD at UNSW, which was focused on the emergence and evolution of epidemic norovirus strains. 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.

Our research group is interested in two major areas of Pathogen Genomics. First, we are trying to better understand the evolutionary mechanisms that drive virus emergence and spread. This work combines high-throughput sequencing and comparative genomics to explore the patterns of genetic variation, evolution and molecular epidemiology of a diverse range of RNA viruses such as norovirus, influenza virus, respiratory syncytial virus, measles virus and ross river virus. We conduct this work in close collaboration with clinicians, entomologists and wildlife health experts, and not only focus on epidemiological ‘population' scales but also at the level of individual hosts, particularly in the context of how viruses evolve within immunocompromised hosts. The second major interest is in the application of unbiased sequencing for pathogen discovery. High-throughput total RNA sequencing offers a new and powerful means of capturing the full diversity of infecting organisms i.e. the "infectome" and our group has been working on different projects to aid in the diagnoses of infectious diseases, better understand microbial interactions and discovery new microbial diversity. Despite its potential, there are a number of practical challenges before such metagenomic approaches can be used reliably in the clinic. One such challenge has been in developing robust pipelines for accurately annotating and summarising metagenomic datasets in real-world practical time-scales.

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Selected publications

• Di Giallonardo F, Kok J, Fernandez M, Carter I, Geoghegan JL, Dwyer DE, Holmes EC, Eden JS. Evolution of Human Respiratory Syncytial Virus (RSV) over Multiple Seasons in New South Wales, Australia. Viruses. 2018;10(9):476
• Shi M, Lin XD, Chen X, Tian JH, Chen LJ, Li K, Wang W, Eden JS, Shen JJ, Liu L, Holmes EC, Zhang YZ. The Origin of Vertebrate RNA Viruses. Nature. 556(7700):197.
• Eden JS, Chisholm RH, Bull RA, White PA, Holmes EC, Tanaka MM. Persistent infections in immunocompromised hosts are rarely sources of new pathogen variants. Virus Evolution. 2017;3(2):vex018.
• Eden JS, Rose K, Ng J, Shi M, Wang Q, Sintchenko V, Holmes EC. Francisella tularensis ssp. holarctica in Ringtail Possums, Australia. Emerging Infectious Diseases. 2017;23(7):1198-201
• Shi M, Lin XD, Tian JH, Chen LJ, Chen X, Li CX, Qin XC, Li J, Cao JP, Eden JS, Buchmann J, Wang W, Xu J, Holmes EC, Zhang YZ. Redefining the invertebrate RNA virosphere. Nature. 2016;540(7634):539-43.
• Eden JS, Read AJ, Duckworth JA, Strive T, Holmes EC. Resolving the origin of rabbit hemorrhagic disease virus: Insights from an investigation of the viral stocks released in Australia. J Virol. 2015;89(23):12217-20.
• Eden JS, Hewitt J, Lim KL, Boni MF, Merif J, Greening G, Ratcliff RM, Holmes EC, Tanaka MM, Rawlinson WD, White PA. The emergence and evolution of the novel epidemic norovirus GII.4 variant Sydney 2012. Virology. 2014;450-451:106-13.
• Eden JS, Tanaka MM, Boni MF, Rawlinson WD, White PA. Recombination within the pandemic norovirus GII.4 lineage. J Virol. 2013;87(11):6270-82.