Associate Professor Jemma Geoghegan

Contact Details
- Phone
- +64 3 470 4696
- jemma.geoghegan@otago.ac.nz
- Position
- Associate Professor
- Department
- Department of Microbiology and Immunology
- Qualifications
- BSc Hons, PhD
- Research summary
- Viral 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
Grimwood, R. M., Fortune-Kelly, G., Holmes, E. C., Ingram, T., & Geoghegan, J. L. (2023). Host specificity shapes fish viromes across lakes on an isolated remote island. Virology, 109884. Advance online publication. doi: 10.1016/j.virol.2023.109884
Miller, A. K., Brosnahan, C. L., Pande, A., Baker, C. F., Geoghegan, J. L., Kitson, J., Gemmell, N. J., & Dowle, E. J. (2023). Formalin-fixed paraffin-embedded (FFPE) samples help to investigate transcriptomic responses in wildlife disease. Molecular Ecology Resources. Advance online publication. doi: 10.1111/1755-0998.13805
Costa, V. A., Bellwood, D. R., Mifsud, J. C. O., Van Brussel, K., Geoghegan, J. L., Holmes, E. C., & Harvey, E. (2023). Limited cross-species virus transmission in a spatially restricted coral reef fish community. Virus Evolution, 9(1), 1-15. doi: 10.1093/ve/vead011
Wierenga, J. R., Morgan, K. J., Hunter, S., Taylor, H. S., Argilla, L. S., Webster, T., Dubrulle, J., Jorge, F., Bostina, M., Burga, L., … Geoghegan, J. L. (2023). A novel gyrovirus is abundant in yellow-eyed penguin (Megadyptes antipodes) chicks with a fatal respiratory disease. Virology, 579, 75-83. doi: 10.1016/j.virol.2022.12.012
Welch, D., Geoghegan, J., & Plank, M. (2022). New Zealand's latest COVID wave is levelling off, with fewer people in hospital than feared. The Conversation. Retrieved from https://theconversation.com/new-zealands-latest-covid-wave-is-levelling-off-with-fewer-people-in-hospital-than-feared-187773
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
Chapter in Book - Research
Costa, V. A., Bellwood, D. R., Mifsud, J. C. O., Van Brussel, K., Geoghegan, J. L., Holmes, E. C., & Harvey, E. (2023). Limited cross-species virus transmission in a spatially restricted coral reef fish community. Virus Evolution, 9(1), 1-15. doi: 10.1093/ve/vead011
Journal - Research Article
Grimwood, R. M., Fortune-Kelly, G., Holmes, E. C., Ingram, T., & Geoghegan, J. L. (2023). Host specificity shapes fish viromes across lakes on an isolated remote island. Virology, 109884. Advance online publication. doi: 10.1016/j.virol.2023.109884
Journal - Research Article
Miller, A. K., Brosnahan, C. L., Pande, A., Baker, C. F., Geoghegan, J. L., Kitson, J., Gemmell, N. J., & Dowle, E. J. (2023). Formalin-fixed paraffin-embedded (FFPE) samples help to investigate transcriptomic responses in wildlife disease. Molecular Ecology Resources. Advance online publication. doi: 10.1111/1755-0998.13805
Journal - Research Article
Wierenga, J. R., Morgan, K. J., Hunter, S., Taylor, H. S., Argilla, L. S., Webster, T., Dubrulle, J., Jorge, F., Bostina, M., Burga, L., … Geoghegan, J. L. (2023). A novel gyrovirus is abundant in yellow-eyed penguin (Megadyptes antipodes) chicks with a fatal respiratory disease. Virology, 579, 75-83. doi: 10.1016/j.virol.2022.12.012
Journal - Research Article
Costa, V. A., Geoghegan, J. L., Holmes, E. C., & Harvey, E. (2022). Genetic reassortment between endemic and introduced Macrobrachium rosenbergii Nodaviruses in the Murray-Darling Basin, Australia. Viruses, 14, 2186. doi: 10.3390/v14102186
Journal - Research Article
Douglas, J., Winter, D., McNeill, A., Carr, S., Bunce, M., French, N., … de Ligt, J., Welch, D., & Geoghegan, J. L. (2022). Tracing the international arrivals of SARS-CoV-2 Omicron variants after Aotearoa New Zealand reopened its border. Nature Communications, 13, 6484. doi: 10.1038/s41467-022-34186-9
Journal - Research Article
Jelley, L., Douglas, J., Ren, X., Winter, D., McNeill, A., Huang, S., French, N., Welch, D., … de Ligt, J., & Geoghegan, J. L. (2022). Genomic epidemiology of Delta SARS-CoV-2 during transition from elimination to suppression in Aotearoa New Zealand. Nature Communications, 13, 4035. doi: 10.1038/s41467-022-31784-5
Journal - Research Article
Mifsud, J. C. O., Gallagher, R. V., Holmes, E. C., & Geoghegan, J. L. (2022). Transcriptome mining expands knowledge of RNA viruses across the plant kingdom. Journal of Virology. Advance online publication. doi: 10.1128/jvi.00260-22
Journal - Research Article
Perry, B. J., Mohammadi Darestani, M., Ara, M. G., Hoste, A., Jandt, J. M., Dutoit, L., … Ingram, T., & Geoghegan, J. L. (2022). Viromes of freshwater fish with lacustrine and diadromous life histories differ in composition. Viruses, 14(2), 257. doi: 10.3390/v14020257
Journal - Research Article
Van Brussel, K., Mahar, J. E., Ortiz-Baez, A. S., Carrai, M., Spielman, D., Boardman, W. S. J., … Geoghegan, J. L., … Holmes, E. C. (2022). Faecal virome of the Australian grey-headed flying fox from urban/suburban environments contains novel coronaviruses, retroviruses and sapoviruses. Virology, 576, 42-51. doi: 10.1016/j.virol.2022.09.002
Journal - Research Article
Waller, S. J., Lamar, S., Perry, B. J., Grimwood, R. M., Holmes, E. C., & Geoghegan, J. L. (2022). Cloacal virome of an ancient host lineage, the tuatara (Sphenodon punctatus), reveals abundant and diverse diet-related viruses. Virology, 575, 43-53. doi: 10.1016/j.virol.2022.08.012
Journal - Research Article
Douglas, J., Geoghegan, J. L., Hadfield, J., Bouckaert, R., Storey, M., Ren, X., … French, N., & Welch, D. (2021). Real-time genomics for tracking severe acute respiratory syndrome coronavirus 2 border incursions after virus elimination, New Zealand. Emerging Infectious Diseases, 27(9), 2361-2368. doi: 10.3201/eid2709.211097
Journal - Research Article
Eichler, N., Thornley, C., Swadi, T., Devine, T., McElnay, C., Sherwood, J., … Brunton, C., … Freeman, J., Berger, S., … Geoghegan, J. L. (2021). Transmission of severe acute respiratory syndrome Coronavirus 2 during border quarantine and air travel, New Zealand (Aotearoa). Emerging Infectious Diseases, 27(5), 1274-1278. doi: 10.3201/eid2705.210514
Journal - Research Article
Geoghegan, J. L., Di Giallonardo, F., Wille, M., Ortiz-Baez, A. S., Costa, V. A., Ghaly, T., … Holmes, E. C. (2021). Virome composition in marine fish revealed by meta-transcriptomics. Virus Evolution, 7(1), veab005. doi: 10.1093/ve/veab005
Journal - Research Article
Geoghegan, J. L., Douglas, J., Ren, X., Storey, M., Hadfield, J., Silander, O. K., … Baker, M. G., Murdoch, D. R., … de Ligt, J. (2021). Use of genomics to track Coronavirus disease outbreaks, New Zealand. Emerging Infectious Diseases, 27(5), 1317-1322. doi: 10.3201/eid2705.204579
Journal - Research Article
Grimwood, R., Holmes, E. C., & Geoghegan, J. L. (2021). A novel rubi-like virus in the Pacific electric ray (Tetronarce californica) reveals the complex evolutionary history of the Matonaviridae. Viruses, 13(4), 585. doi: 10.3390/v13040585
Journal - Research Article
Holmes, E. C., Goldstein, S. A., Rasmussen, A. L., Robertson, D. L., Crits-Christoph, A., Wertheim, J. O., … Geoghegan, J. L., … Rambaut, A. (2021). The origins of SARS-CoV-2: A critical review. Cell, 181, 4848-4856. doi: 10.1016/j.cell.2021.08.017
Journal - Research Article
Miller, A. K., Mifsud, J. C. O., Costa, V. A., Grimwood, R. M., Kitson, J., Baker, C., … Gemmell, N. J., & Geoghegan, J. L. (2021). Slippery when wet: Cross-species transmission of divergent coronaviruses in bony and jawless fish and the evolutionary history of the Coronaviridae. Virus Evolution, 7(2), veab050. doi: 10.1093/ve/veab050
Journal - Research Article
Nguyen, T., Adnan, M., Nguyen, B. P., de Ligt, J., Geoghegan, J. L., Dean, R., … Baker, M. G., … Murdoch, D. R., … Simpson, C. R. (2021). COVID-19 vaccine strategies for Aotearoa New Zealand: A mathematical modelling study. Lancet Regional Health: Western Pacific, 15, 100256. doi: 10.1016/j.lanwpc.2021.100256
Journal - Research Article
Nielsen, D. A., Fierer, N., Geoghegan, J. L., Gillings, M. R., Gumerov, V., Madin, J. S., … Westoby, M. (2021). Aerobic bacteria and archaea tend to have larger and more versatile genomes. Oikos, 130, 501-511. doi: 10.1111/oik.07912
Journal - Research Article
O'Toole, Á., Hill, V., Pybus, O. G., Watts, A., Bogoch, I. I., Khan, K., … Geoghegan, J. L., … Kraemer, M. U. G. (2021). Tracking the international spread of SARS-CoV-2 lineages B.1.1.7 and B.1.351/501Y-V2 [version 1; peer review: 3 approved]. Wellcome Open Research, 6. doi: 10.12688/wellcomeopenres.16661.1
Journal - Research Article
Swadi, T., Geoghegan, J. L., Devine, T., McElnay, C., Sherwood, J., Shoemack, P., … de Ligt, J. (2021). Genomic evidence of in-flight transmission of SARS-CoV-2 despite predeparture testing. Emerging Infectious Diseases, 27(3). doi: 10.3201/eid2703.204714
Journal - Research Article
Wille, M., Geoghegan, J. L., & Holmes, E. C. (2021). How accurately can we assess zoonotic risk? PLoS Biology, 19(4), e3001135. doi: 10.1371/journal.pbio.3001135
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, 6(2), veaa065. doi: 10.1093/ve/veaa065
Journal - Research Article
Di Giallonardo, F., Pinto, A. N., Keen, P., Shaik, A., Carrera, A., Salem, H., … Geoghegan, J. L., … and the NSW HIV Prevention Partnership Project. (2020). Subtype-specific differences in transmission cluster dynamics of HIV-1 B and CRF01_AE in New South Wales, Australia. Journal of the International AIDS Society, 23, e25655. doi: 10.1002/jia2.25655
Journal - Research Article
Geoghegan, J. L., Ren, X., Storey, M., Hadfield, J., Jelley, L., Jefferies, S., … Baker, M. G., Murdoch, D. R., … de Ligt, J. (2020). Genomic epidemiology reveals transmission patterns and dynamics of SARS-CoV-2 in Aotearoa New Zealand. Nature Communications, 11(1), 6351. doi: 10.1038/s41467-020-20235-8
Journal - Research Article
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
Journal - Research Article
Madin, J. S., Nielson, D. A., Brbic, M., Corkrey, R., Danko, D., Edwards, K., … Geoghegan, J. L., … Westoby, M. (2020). A synthesis of bacterial and archaeal phenotypic trait data. Scientific Data, 7, 170. doi: 10.1038/s41597-020-0497-4
Journal - Research Article
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
Journal - Research Article
Turnbull, O. M. H., Ortiz-Baez, A. S., Eden, J.-S., Shi, M., Williamson, J. E., Gaston, T. F., … Geoghegan, J. L. (2020). Meta-transcriptomic identification of divergent Amnoonviridae in fish. Viruses, 12(11), 1254. doi: 10.3390/v12111254
Journal - Research Article
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
Journal - Research Article
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
Journal - Research Article
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
Journal - Research Article
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
Journal - Research Article
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
Journal - Research Article
Geoghegan, J. L., & Holmes, E. C. (2017). Predicting virus emergence amid evolutionary noise. Open Biology, 7(10), 170189. doi: 10.1098/rsob.170189
Journal - Research Article
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
Journal - Research Article
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
Journal - Research Article
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
Journal - Research Article
Geoghegan, J. L. (2016). Predicting pandemics. Australasian Science, (October), 30-32.
Journal - Research Article
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
Journal - Research Article
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
Journal - Research Article
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
Journal - Research Article
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
Journal - Research Article
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
Journal - Research Article
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
Journal - Research Article
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
Journal - Research Article
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
Journal - Research Article
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
Journal - Research Article
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
Journal - Research Article
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
Journal - Research Article
Alcantara, L. C. J., Amenga-Etego, L., Andersson, R., Bhaumik, M., Choi, Y. K., Decaluwe, H., Geoghegan, J., … Fang, Y. S. C. (2022). Methods for fighting emerging pathogens. Nature Methods. Advance online publication. doi: 10.1038/s41592-022-01441-2
Journal - Research Other
Geoghegan, J., Welch, D., & de Ligt, J. (2022). Should we worry about the XE variant? Maybe not yet, but 'hybrids' will become more frequent as COVID evolves. The Conversation. Retrieved from https://theconversation.com/should-we-worry-about-the-xe-variant-maybe-not-yet-but-hybrids-will-become-more-frequent-as-covid-evolves-180672
Journal - Research Other
Welch, D., Geoghegan, J., & Plank, M. (2022). New Zealand's latest COVID wave is levelling off, with fewer people in hospital than feared. The Conversation. Retrieved from https://theconversation.com/new-zealands-latest-covid-wave-is-levelling-off-with-fewer-people-in-hospital-than-feared-187773
Journal - Research Other
Welch, D., Hadfield, J., Geoghegan, J., de Ligt, J., & Bunce, M. (2022). As New Zealand's Omicron infections rise rapidly, genome surveillance is shifting gears. The Conversation. Retrieved from https://theconversation.com/as-new-zealands-omicron-infections-rise-rapidly-genome-surveillance-is-shifting-gears-177441
Journal - Research Other
Geoghegan, J. L., Moreland, N. J., Le Gros, G., & Ussher, J. E. (2021). New Zealand's science-led response to the SARS-CoV-2 pandemic. Nature Immunology, 22, 262-263. doi: 10.1038/s41590-021-00872-x
Journal - Research Other
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
Journal - Research Other
Geoghegan, J. L., & Holmes, E. C. (2018). Evolutionary virology at 40. Genetics, 210(4), 1151-1162. doi: 10.1534/genetics.118.301556
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
Journal - Research Other
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
Journal - Research Other