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Otago Medical School staff profiles

Dr Jemma Geoghegan

PositionSenior Lecturer
DepartmentDepartment of Microbiology and Immunology
Research summaryViral evolutionary biology

Research

I am an evolutionary biologist and virologist with a strong research focus on emerging infectious disease. My research focuses on determining the fundamental patterns and processes of viral evolution, ecology and emergence.

My research involves using metagenomics to reveal the diversity, structure and evolution of the virosphere; examining the evolution of major viral infections; and developing new analytical and computational approaches to analyse aspects of the virus evolution.

Publications

Campbell, S. J., Ashley, W., Gil-Fernandez, M., Newsome, T. M., Di Giallonardo, F., Ortiz-Baez, A. S., … Geoghegan, J. L. (2020). Red fox viromes in urban and rural landscapes. Virus Evolution. Advance online publication.

Parry, R., Wille, M., Turnbull, O. M. H., Geoghegan, J. L., & Holmes, E. C. (2020). Divergent influenza-like viruses of amphibians and fish support an ancient evolutionary association. Viruses, 12(9), 1042. doi: 10.3390/v12091042

Ghaly, T. M., Geoghegan, J. L., Tetu, S. G., & Gillings, M. R. (2020). The peril and promise of integrons: Beyond antibiotic resistance. Trends in Microbiology, 28(6), 455-464. doi: 10.1016/j.tim.2019.12.002

Ghaly, T. M., Geoghegan, J. L., Alroy, J., & Gillings, M. R. (2019). High diversity and rapid spatial turnover of integron gene cassettes in soil. Environmental Microbiology, 21(5), 1567-1574. doi: 10.1111/1462-2920.14551

Geoghegan, J. L., & Holmes, E. C. (2018). The phylogenomics of evolving virus virulence. Nature Reviews Genetics, 19(12), 756-769. doi: 10.1038/s41576-018-0055-5

Chapter in Book - Research

Geoghegan, J. L. (2014). Inheritance of epigenome variants across generations and its implications on the emergence of phenotypic novelties during evolution. In T. Tollefsbol (Ed.), Transgenerational epigenetics: Evidence and debates. (pp. 187-194). London, UK: Academic Press. doi: 10.1016/B978-0-12-405944-3.00015-5

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Journal - Research Article

Campbell, S. J., Ashley, W., Gil-Fernandez, M., Newsome, T. M., Di Giallonardo, F., Ortiz-Baez, A. S., … Geoghegan, J. L. (2020). Red fox viromes in urban and rural landscapes. Virus Evolution. Advance online publication.

Ghaly, T. M., Geoghegan, J. L., Tetu, S. G., & Gillings, M. R. (2020). The peril and promise of integrons: Beyond antibiotic resistance. Trends in Microbiology, 28(6), 455-464. doi: 10.1016/j.tim.2019.12.002

Parry, R., Wille, M., Turnbull, O. M. H., Geoghegan, J. L., & Holmes, E. C. (2020). Divergent influenza-like viruses of amphibians and fish support an ancient evolutionary association. Viruses, 12(9), 1042. doi: 10.3390/v12091042

Ghaly, T. M., Geoghegan, J. L., Alroy, J., & Gillings, M. R. (2019). High diversity and rapid spatial turnover of integron gene cassettes in soil. Environmental Microbiology, 21(5), 1567-1574. doi: 10.1111/1462-2920.14551

Geoghegan, J. L., & Holmes, E. C. (2018). The phylogenomics of evolving virus virulence. Nature Reviews Genetics, 19(12), 756-769. doi: 10.1038/s41576-018-0055-5

Tong, K. J., Duchêne, D. A., Geoghegan, J. L., & Ho, S. Y. W. (2018). A comparison of methods for estimating substitution rates from ancient DNA sequence data. BMC Evolutionary Biology, 18(1), 70. doi: 10.1186/s12862-018-1192-3

Geoghegan, J. L., Saavedra, A. F., Duchêne, S., Sullivan, S., Barr, I., & Holmes, E. C. (2018). Continental synchronicity of human influenza virus epidemics despite climactic variation. PLoS Pathogens, 14(1), e1006780. doi: 10.1371/journal.ppat.1006780

Di Giallonardo, F., Kok, J., Fernandez, M., Carter, I., Geoghegan, J. L., Dwyer, D. E., … Eden, J.-S. (2018). Evolution of human respiratory syncytial virus (RSV) over multiple seasons in New South Wales, Australia. Viruses, 10(9), 476. doi: 10.3390/v10090476

Geoghegan, J. L., Duchêne, S., & Holmes, E. C. (2017). Comparative analysis estimates the relative frequencies of co-divergence and cross-species transmission within viral families. PLoS Pathogens, 13(2), e1006215. doi: 10.1371/journal.ppat.1006215

Geoghegan, J. L., & Holmes, E. C. (2017). Predicting virus emergence amid evolutionary noise. Open Biology, 7(10), 170189. doi: 10.1098/rsob.170189

Geoghegan, J. L. (2016). Predicting pandemics. Australasian Science, (October), 30-32.

Duchêne, S., Geoghegan, J. L., Holmes, E. C., & Ho, S. Y. W. (2016). Estimating evolutionary rates using time-structured data: A general comparison of phylogenetic methods. Bioinformatics, 32(22), 3375-3379. doi: 10.1093/bioinformatics/btw421

Geoghegan, J. L., Senior, A. M., Di Giallonardo, F., & Holmes, E. C. (2016). Virological factors that increase the transmissibility of emerging human viruses. PNAS, 113(15), 4170-4175. doi: 10.1073/pnas.1521582113

Di Giallonardo, F., Geoghegan, J. L., Docherty, D. E., McLean, R. G., Zody, M. C., Qu, J., … Holmes, E. C. (2016). Fluid spatial dynamics of West Nile virus in the United States: Rapid spread in a permissive host environment. Journal of Virology, 90(2), 862-872. doi: 10.1128/JVI.02305-15

Geoghegan, J. L., Senior, A. M., & Holmes, E. C. (2016). Pathogen population bottlenecks and adaptive landscapes: Overcoming the barriers to disease emergence. Proceedings of the Royal Society B, 283(1837), 20160727. doi: 10.1098/rspb.2016.0727

Geoghegan, J. L., Le Van, T., Kühnert, D., Halpin, R., Lin, X., Simenauer, A., … Van Doorn, H. R. (2015). Phylodynamics of enterovirus A71-associated hand, foot, and mouth disease in Viet Nam. Journal of Virology, 89(17), 8871-8879. doi: 10.1128/JVI.00706-15

Le Van, T., Nguyen Thi, K. T., Tran, T. T., Tran, T. N., Hoang, M. T. V., Sabanathan, S., … Geoghegan, J. L., … Van Doorn, H. R. (2015). A generic assay for whole-genome amplification and deep sequencing of enterovirus A71. Journal of Virological Methods, 30-36. doi: 10.1016/j.jviromet.2015.02.011

Geoghegan, J. L., Walker, P. J., Duchemin, J.-P., Jeanne, I., & Holmes, E. C. (2014). Seasonal drivers of the epidemiology of arthropod-borne viruses in Australia. PLoS Neglected Tropical Diseases, 8(11), e3325. doi: 10.1371/journal.pntd.0003325

Dalziel, B. D., Huang, K., Geoghegan, J. L., Arinaminpathy, N., Dubovi, E. J., Grenfell, B. T., … Parish, C. R. (2014). Contact heterogeneity, rather than transmission efficiency, limits the emergence and spread of canine influenza virus. PLoS Pathogens, 10(10), e1004455. doi: 10.1371/journal.ppat.1004455

Lopes, A. M., Capucci, L., Gavier-Widén, D., LeGall-Reculé, G., Brocchi, E., Barbieri, I., … Geoghegan, J. L., … Abrantes, J. (2014). Molecular evolution and antigenic variation of European brown hare syndrome virus (EBHSV). Virology, 104-112. doi: 10.1016/j.virol.2014.08.002

Geoghegan, J. L., & Spencer, H. G. (2013). Exploring epiallele stability in a population-epigenetic model. Theoretical Population Biology, 83, 136-144. doi: 10.1016/j.tpb.2012.09.001

Geoghegan, J. L., & Spencer, H. G. (2013). The adaptive invasion of epialleles in a heterogeneous environment. Theoretical Population Biology, 88, 1-8. doi: 10.1016/j.tpb.2013.05.001

Geoghegan, J. L., & Spencer, H. G. (2013). The evolutionary potential of paramutation: A population-epigenetic model. Theoretical Population Biology, 88, 9-19. doi: 10.1016/j.tpb.2013.05.003

Geoghegan, J. L., & Spencer, H. G. (2012). Population-epigenetic models of selection. Theoretical Population Biology, 81(3), 232-242. doi: 10.1016/j.tpb.2011.08.001

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Journal - Research Other

Geoghegan, J. L., Pirotta, V., Harvey, E., Smith, A., Buchman, J. P., Ostrowski, M., … Holmes, E. C. (2018). Virological sampling of inaccessible wildlife with drones [Communication]. Viruses, 10(6), 300. doi: 10.3390/v10060300

Geoghegan, J. L., & Holmes, E. C. (2018). Evolutionary virology at 40. Genetics, 210(4), 1151-1162. doi: 10.1534/genetics.118.301556

Duchene, S., Duchene, D. A., Geoghegan, J. L., Dyson, Z. A., Hawkey, J., & Holt, K. E. (2018). Inferring demographic parameters in bacterial genomic data using Bayesian and hybrid phylogenetic methods. BMC Evolutionary Biology, 18(1), 95. doi: 10.1186/s12862-018-1210-5

Duchêne, S., Duchêne, D. A., Di Giallonardo, F., Eden, J.-S., Geoghegan, J. L., Holt, K. E., … Holmes, E. C. (2016). Cross-validation to select Bayesian hierarchical models in phylogenetics. BMC Evolutionary Biology, 16(1), 115. doi: 10.1186/s12862-016-0688-y

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