Professor Jemma Geoghegan

Evolutionary Virologist
Rutherford Discovery Fellow

Email jemma.geoghegan@otago.ac.nz
Tel +64 3 470 4696

Teaching

MICR 463 Trends in Microbiology (Convenor)
MICR 461 Molecular Microbiology
GENE 221 Molecular and Microbial Genetics
MICR 336 Microbial Ecology
MICR 360 Research Perspectives

BSc Hons (First class) University of Strathclyde, Scotland; PhD, University of Otago

Year of appointment: 2020

Previous academic positions

Lecturer at Macquarie University (2017-2020)
Postdoctoral Research Fellow at the University of Sydney (2013-2017)
Research Associate at New York University (2012-2013)

Current research

My research involves using metagenomics to reveal the diversity, structure and evolution of the virosphere; examining the evolution of major viral infections, including SARS-CoV-2; and developing new analytical and computational approaches to analyse aspects of virus evolution.

Research interests

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.

Postgraduate opportunities available

PhD scholarships are available for talented students interested in studying aspects of virus evolution.

The PhD position requires the applicant to be eligible for admission to the PhD programme at the University of Otago and to be eligible for a scholarship. A GPA of 7.5 or greater and demonstration of proficiency in English are essential.

Search the Scholarships Database

Interested candidates with a BSc(Hons) or MSc degree are highly encouraged to get in touch.

Publications

French, N. P., Maxwell, H., Baker, M. G., Callaghan, F., Dyet, K., Geoghegan, J. L., … Kvalsvig, A., Russell, E., Scott, P., … Plank, M. J. (2025). Preparing for the next pandemic: Insights from Aotearoa New Zealand's Covid-19 response. Lancet Regional Health: Western Pacific, 56, 101525. doi: 10.1016/j.lanwpc.2025.101525 Journal - Research Other

Waller, S. J., Wierenga, J. R., Heremia, L., Darnley, J. A., de Vries, I., Dubrulle, J., Robinson, Z., Miller, A. K., … Ellenberg, U., … Keys, B. C., … Mattern, T., … Waipoua, T. A., … Geoghegan, J. L. (2025). Avian influenza virus surveillance across New Zealand and its subantarctic islands detects H1N9 in migratory shorebirds, but not 2.3.4.4b HPAI H5N1. Influenza & Other Respiratory Viruses, 19, e70099. doi: 10.1111/irv.70099 Journal - Research Other

Taylor, J. T., Lee, V., Dearlove, T., Jolly, M., Wierenga, J. R., Dubrulle, J., Hodgkinson-Bean, J., … French, N., … Geoghegan, J. L. (2025). A metagenomic investigation into Apteryx rowi dermatosis identifies multiple novel viruses and a highly abundant nematode. Journal of Wildlife Diseases. Advance online publication. doi: 10.7589/jwd-d-24-00115 Journal - Research Article

Huang, Q. S., Wood, T., Aminisani, N., Kvalsvig, A., Baker, M. G., Nghiem, N., … Jelley, L., … Geoghegan, J. L., … Dowell, T., … McIntyre, P., … on behalf of the SHIVERS investigation team. (2025). Comparison of the incidence and risk factors of COVID-19 and influenza associated acute respiratory illnesses: Results of the SHIVERS-II, III, IV prospective community cohort study. Journal of Infectious Diseases. Advance online publication. doi: 10.1093/infdis/jiaf097 Journal - Research Article

Costa, V. A., Bellwood, D. R., Mifsud, J. C. O., Geoghegan, J. L., Harvey, E., & Holmes, E. C. (2025). Limited similarity in microbial composition among coral reef fishes from the Great Barrier Reef, Australia. FEMS Microbiology Ecology. Advance online publication. doi: 10.1093/femsec/fiaf016 Journal - Research Article

2025

Journal - Research Article

Hills, F. R., Geoghegan, J. L., & Bostina, M. (2025). Architects of infection: A structural overview of SARS-related coronavirus spike glycoproteins. Virology, 110383. Advance online publication. doi: 10.1016/j.virol.2024.110383

Journal - Research Other

2024

Journal - Research Article

French, R. K., Anderson, S., Cain, K., Digby, A., Greene, T. C., Miskelly, C. M., … Geoghegan, J. L., & Holmes, E. C. (2024). Diversity and cross-species transmission of viruses in a remote island ecosystem: Implications for wildlife conservation. Virus Evolution. Advance online publication. doi: 10.1093/ve/veae113

Jelley, L., Douglas, J., O'Neill, M., Berquist, K., Claasen, A., Wang, J., … McIntyre, P., Dowell, T., … Geoghegan, J. L. (2024). Spatial and temporal transmission dynamics of respiratory syncytial virus in New Zealand before and after the COVID-19 pandemic. Nature Communications, 15, 9758. doi: 10.1038/s41467-024-53998-5

Grimwood, R. M., Waller, S. J., Wierenga, J. R., Lim, L., Dubrulle, J., Holmes, E. C., & Geoghegan, J. L. (2024). Viromes of Antarctic fish resemble the diversity found at lower latitudes. Virus Evolution, 10(1), veae050. doi: 10.1093/ve/veae050

Grimwood, R. M., Reyes, E. M. R., Cooper, J., Welch, J., Taylor, G., Makan, T., … Dubrulle, J., … Geoghegan, J. L. (2024). From islands to infectomes: Host-specific viral diversity among birds across remote islands. BMC Ecology & Evolution, 24(1), 84. doi: 10.1186/s12862-024-02277-4

Waller, S. J., Butcher, R. G., Lim, L., McInnes, K., Holmes, E. C., & Geoghegan, J. L. (2024). The radiation of New Zealand’s skinks and geckos is associated with distinct viromes. BMC Ecology & Evolution, 24, 81. doi: 10.1186/s12862-024-02269-4

Waller, S. J., Egan, E., Crow, S., Charsley, A., Lokman, P. M., Williams, E. K., … Geoghegan, J. L. (2024). Host and geography impact virus diversity in New Zealand’s longfin and shortfin eels. Archives of Virology, 169, 85. doi: 10.1007/s00705-024-06019-1

Waller, S. J., Tortosa, P., Thurley, T., O'Donnell, C. F. J., Jackson, R., Dennis, G., Grimwood, R., … Geoghegan, J. L. (2024). Virome analysis of New Zealand's bats reveals cross-species viral transmission among the Coronaviridae. Virus Evolution, 10(1), veae008. doi: 10.1093/ve/veae008

Huang, Q. S., Turner, N., Wood, T., Anglemyer, A., McIntyre, P., Aminisani, N., Dowell, T., … Geoghegan, J., … Jelley, L., … Baker, M. G., Kvalsvig, A., … Webby, R. J. (2024). Impact of the COVID-19 related border restrictions on influenza and other common respiratory viral infections in New Zealand. Influenza & Other Respiratory Viruses, 18, e13247. doi: 10.1111/irv.13247

Journal - Research Other

Chang, W.-S., Harvey, E., Mahar, J. E., Firth, C., Shi, M., Simon-Loriere, E., Geoghegan, J. L., & Wille, M. (2024). Improving the reporting of metagenomic virome-scale data. Communications Biology, 7, 1687. doi: 10.1038/s42003-024-07212-3

Waller, S., French, N., & Geoghegan, J. L. (2024). Aotearoa's first case of highly pathogenic avian influenza: Heightened awareness and surveillance essential for early detection. The Briefing, (11 December). Retrieved from https://www.phcc.org.nz/briefing/aotearoas-first-case-highly-pathogenic-avian-influenza-heightened-awareness-and

Baker, M., Potter, J. D., French, N., Geoghegan, J. L., Wilson, N., Mansoor, O., … Webby, R. (2024). Potential for an avian influenza pandemic: Time for NZ to ramp up preparedness. The Briefing, (15 May). Retrieved from https://www.phcc.org.nz/briefing/potential-avian-influenza-pandemic-time-nz-ramp-preparedness

Conference Contribution - Published proceedings: Abstract

Wierenga, J., Morgan, K., Hunter, S., Taylor, H., Argilla, L., Webster, T., Burga, L., Bostina, M., Lim, L., … Geoghegan, J. (2024). Finding the causative agents of infectious diseases affecting hoiho (yellow-eyed penguins) in New Zealand. New Zealand Journal of Zoology, 51(3-4), (pp. 440). doi: 10.1080/03014223.2024.2332118

Conference Contribution - Poster Presentation (not in published proceedings)

Dubrulle, J., Poulin, R., Salloum, P., & Geoghegan, J. L. (2024, September). Spatial variation in the microbiome of the sandhopper Bellochestia quoyana endemic to New Zealand. Poster session presented at the Queenstown Research Week (QRW) Pathogen Genomics Meeting, Queenstown, New Zealand.

2023

Journal - Research Article

Wierenga, J. R., Grimwood, R., Taylor, H. S., Hunter, S., Argilla, L. S., Webster, T., Lim, L., French, R., … Jorge, F., Bostina, M., Burga, L., … Geoghegan, J. L. (2023). Total infectome investigation of diphtheritic stomatitis in yellow-eyed penguins (Megadyptes antipodes) reveals a novel and abundant megrivirus. Veterinary Microbiology, 286, 109895. doi: 10.1016/j.vetmic.2023.109895

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, 587, 109884. 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

Journal - Research Other

Baker, M., Crump, J., Kvalsvig, A., Geoghegan, J., Tukuitonga, C., Brewerton, M., Kerr, J., & Wilson, N. (2023). Why we need an Aotearoa Centre for Disease Control (CDC). The Briefing, (16 November). Retrieved from https://www.phcc.org.nz/briefing/why-we-need-aotearoa-centre-disease-control-cdc

Baker, M. G., Kvalsvig, A., Plank, M. J., Geoghegan, J. L., Wall, T., Tukuitonga, C., Summers, J., Bennett, J., Kerr, J., Turner, N., … Betty, B., … French, N., & Wilson, N. (2023). Continued mitigation needed to minimise the high health burden from COVID-19 in Aotearoa New Zealand. New Zealand Medical Journal/Te ara tika o te hauora hapori, 136(1583), 67-91. Retrieved from https://journal.nzma.org.nz/

Bunce, M., Geoghegan, J. L., Winter, D., de Ligt, J., & Wiles, S. (2023). Exploring the depth and breadth of the genomics toolbox during the COVID-19 pandemic: Insights from Aotearoa New Zealand. BMC Medicine, 21, 213. doi: 10.1186/s12916-023-02909-4

Conference Contribution - Published proceedings: Abstract

Miller, A., Baker, C., Brosnahan, C., Dowle, E., Gemmell, N., Geoghegan, J., … Pande, A. (2023). Formalin-fixed paraffin-embedded (FFPE) samples help to investigate potential wildlife disease. Proceedings of the Genetics Otago (GO) Annual Symposium & Workshops. Retrieved from https://blogs.otago.ac.nz/go

Waller, S. J., Tortosa, P., Thurley, T., O'Donnell, C., Jackson, R., Dennis, G., Grimwood, R. M., … Geoghegan, J. L. (2023). Exploring the diverse viromes of New Zealand’s bats. Proceedings of the Genetics Otago (GO) Annual Symposium & Workshops. Retrieved from https://blogs.otago.ac.nz/go

Grimwood, R. M., Welch, J., Taylor, G., Emmitt, T., Thurley, T., Makan, T., … Dubrulle, J., … Geoghegan, J. L. (2023). From islands to infectomes: The interplay between host taxonomy and environment on microbial diversity among birds across remote islands. Proceedings of the Genetics Otago (GO) Annual Symposium & Workshops. Retrieved from https://blogs.otago.ac.nz/go

Conference Contribution - Verbal presentation and other Conference outputs

Geoghegan, J. (2023, August). The role of host ecology in shaping the virome. Verbal presentation at the 33rd Queenstown Molecular Biology Meeting (QMB), Queenstown, New Zealand.

2022

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

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

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

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

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

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, 96(24). doi: 10.1128/jvi.00260-22

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 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

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

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, 19, 395-397. doi: 10.1038/s41592-022-01441-2

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

Conference Contribution - Published proceedings: Abstract

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. Proceedings of the Genetics Otago (GO) Annual Symposium. Retrieved from https://blogs.otago.ac.nz/go

Fox-Lewis, A., Williamson, F., Harrower, J., Ren, X., Sonder, G. J. B., McNeill, A., … Geoghegan, J. L. (2022). Airborne transmission of SARS-CoV-2 lineage B.1.617.2 (Delta variant) within a tightly monitored isolation facility. Pathology, 54(Suppl. 1), (pp. S32). doi: 10.1016/j.pathol.2021.12.103

Conference Contribution - Poster Presentation (not in published proceedings)

Wierenga, J. R., Morgan, K. J., Hunter, S., Taylor, H., McInnes, K., & Geoghegan, J. L. (2022, August). Investigation of a causative agent for Respiratory Distress Syndrome in neonatal hoiho. Poster session presented at the Webster Centre for Infectious Diseases Satellite Meeting: Queenstown Research Week, Queenstown, New Zealand.

Grimwood, R. M., Holmes, E. C., & Geoghegan, J. L. (2022, August). A novel rubi-like virus in the Pacific Electric Ray (Tetronarce californica) reveals the complex evolutionary history of the Matonaviridae. Poster session presented at the Webster Centre for Infectious Diseases Satellite Meeting: Queenstown Research Week, Queenstown, New Zealand.

Waller, S. J., Lamar, S., Perry, B. J., Grimwood, R. M., Holmes, E. C., & Geoghegan, J. L. (2022, August). Cloacal virome of an ancient host lineage, the tuatara (Sphenodon punctatus), reveals abundant and diverse diet-related viruses. Poster session presented at the Webster Centre for Infectious Diseases Satellite Meeting: Queenstown Research Week, Queenstown, New Zealand.

Other Research Output

Geoghegan, J. (2022, March). COVID-19 in Aotearoa: Insights from genomics. Alumni Event, University of Otago, [Online]. [Research Presentation].

2021

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

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

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

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

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

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

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

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

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

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

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

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 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

Conference Contribution - Published proceedings: Abstract

Geoghegan, J. (2021). Tracking COVID-19 in New Zealand using genomics. Proceedings of the 16th Congress of the Federation of Asian & Oceanic Biochemists & Molecular Biologists (FAOBMB). (pp. 200). Retrieved from https://www.faobmb2021.org

Conference Contribution - Verbal presentation and other Conference outputs

Geoghegan, J. (2021, July). SARS-CoV-2 in New Zealand: Insights from genomics. Verbal presentation at the Association for Women in the Sciences (AWIS) Triennial Conference: Embracing Diversity, Dunedin, New Zealand.

2020

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

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

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

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

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

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

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

Conference Contribution - Verbal presentation and other Conference outputs

Geoghegan, J. L. (2020, December). Genomic epidemiology of COVID-19 in Aotearoa [Invited]. Verbal presentation at the 6th One Health Aotearoa (OHA) Symposium, [Online].

Geoghegan, J. (2020, September). Genomics of COVID19 in New Zealand. Verbal presentation at the Queenstown Molecular Biology (QMB) Meetings, [Online].

2019

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

2018

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

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

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., 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 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

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

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

2017

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

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

2016

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

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

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

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

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 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

2015

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

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

Conference Contribution - Published proceedings: Abstract

Geoghegan, J. L., Holmes, E. C., Van Doorn, R., & Le Van, T. (2015). Evolution and phylodynamics of enterovirus A71. Journal of Clinical Virology, 70, (pp. 55). doi: 10.1016/j.jcv.2015.07.020

Working Paper; Discussion Paper; Technical Report

Saavedra, A. F., Wood, S., Geoghegan, J. L., Holmes, E., & Durrant-Whyte, H. (2015). Modelling the spread of influenza in Western Australia. Semantic Scholar. Retrieved from https://www.semanticscholar.org/paper/Modelling-the-spread-of-influenza-in-Western-%E2%88%97-Saavedra-Wood/541a27c5a8d929750f9ec125bf3867770cdfd0e0

2014

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

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

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

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

2013

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

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). Exploring epiallele stability in a population-epigenetic model. Theoretical Population Biology, 83, 136-144. doi: 10.1016/j.tpb.2012.09.001

Awarded Doctoral Degree

Geoghegan, J. (2013). Modelling selection under soft inheritance (PhD). University of Otago. Retrieved from http://hdl.handle.net/10523/3718

2012

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

Conference Contribution - Verbal presentation and other Conference outputs

Spencer, H. G., & Geoghegan, J. L. (2012, November). Population epigenetics: How does natural selection act on epigenetic variation? Verbal presentation at the Gravida Annual Science Symposium: What Makes the Best Start for a Healthy Life? Palmerston North, New Zealand.

2010

Conference Contribution - Verbal presentation and other Conference outputs

Geoghegan, J. (2010, November). Transgenerational influences: Models of population epigenetics. Verbal presentation at the Genetics Otago Symposium, Dunedin, New Zealand.