Contact Details
- Phone
- +64 3 470 4696
- jemma.geoghegan@otago.ac.nz
- Position
- 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
Hoggard, M., Gios, E., Tee, H. S., Geoghegan, J. L., & Handley, K. M. (2026). DNA viruses are constrained to ecological niches and share similar environmental adaptations with hosts. Nature Communications. Advance online publication. doi: 10.1038/s41467-026-73439-9 Journal - Research Article
Guhlin, J., Wierenga, J. R., Douglas, J., Swindells-Wallace, P., Langsbury, H., Webster, T., Young, M. J., … Alden, B., Ruru, T. T., … van Heezik, Y., Seddon, P. J., … Dearden, P. K., & Geoghegan, J. L. (2026). Population genomics of yellow-eyed penguins uncovers subspecies divergence and candidate genes linked to respiratory distress syndrome. Nature Ecology & Evolution. Advance online publication. doi: 10.1038/s41559-026-03062-w Journal - Research Article
de Vries, I. F., Waller, S. J., French, R. K., Grimwood, R. M., & Geoghegan, J. L. (2026). Longitudinal sampling of New Zealand cockles (Austrovenus stutchburyi) reveals high viral diversity and taxa-specific responses to environmental factors. FEMS Microbiology Ecology, 102(5), fiag033. doi: 10.1093/femsec/fiag033 Journal - Research Article
Taylor, H. S., Eames, M., Bestbier, M., Hunter, S., Weir, J. S., O'Connell, J., … Waller, S. J., Geoghegan, J. L., … Roe, W. D. (2026). A large mortality event in New Zealand fur seals (Arctocephalus forsteri) caused by a divergent canine distemper virus. Veterinary Microbiology, 316, 111000. doi: 10.1016/j.vetmic.2026.111000 Journal - Research Article
French, R. K., Pichlmueller, F., Waller, S. J., Dubrulle, J., Tuxford, J., Veale, A., & Geoghegan, J. L. (2026). Viral surveillance of invasive mammals in New Zealand reveals unique viral lineages reflecting their introduction history. Genetics & Molecular Biology, 100(1), e01440-25. doi: 10.1128/jvi.01440-25 Journal - Research Article
2026
Journal - Research Article
Hoggard, M., Gios, E., Tee, H. S., Geoghegan, J. L., & Handley, K. M. (2026). DNA viruses are constrained to ecological niches and share similar environmental adaptations with hosts. Nature Communications. Advance online publication. doi: 10.1038/s41467-026-73439-9
Guhlin, J., Wierenga, J. R., Douglas, J., Swindells-Wallace, P., Langsbury, H., Webster, T., Young, M. J., … Alden, B., Ruru, T. T., … van Heezik, Y., Seddon, P. J., … Dearden, P. K., & Geoghegan, J. L. (2026). Population genomics of yellow-eyed penguins uncovers subspecies divergence and candidate genes linked to respiratory distress syndrome. Nature Ecology & Evolution. Advance online publication. doi: 10.1038/s41559-026-03062-w
de Vries, I. F., Waller, S. J., French, R. K., Grimwood, R. M., & Geoghegan, J. L. (2026). Longitudinal sampling of New Zealand cockles (Austrovenus stutchburyi) reveals high viral diversity and taxa-specific responses to environmental factors. FEMS Microbiology Ecology, 102(5), fiag033. doi: 10.1093/femsec/fiag033
Taylor, H. S., Eames, M., Bestbier, M., Hunter, S., Weir, J. S., O'Connell, J., … Waller, S. J., Geoghegan, J. L., … Roe, W. D. (2026). A large mortality event in New Zealand fur seals (Arctocephalus forsteri) caused by a divergent canine distemper virus. Veterinary Microbiology, 316, 111000. doi: 10.1016/j.vetmic.2026.111000
French, R. K., Pichlmueller, F., Waller, S. J., Dubrulle, J., Tuxford, J., Veale, A., & Geoghegan, J. L. (2026). Viral surveillance of invasive mammals in New Zealand reveals unique viral lineages reflecting their introduction history. Genetics & Molecular Biology, 100(1), e01440-25. doi: 10.1128/jvi.01440-25
2025
Journal - Research Article
Ayriss, N., West, A. G., French, R. K., Geoghegan, J. L., Chatterton, J., Digby, A., … Taylor, M. W. (2025). Influence of developmental stage on the antibiotic resistome and virome of the critically endangered kākāpō (Strigops habroptilus). Frontiers in Microbiology, 16, 1654781. doi: 10.3389/fmicb.2025.1654781
Grimwood, R. M., Zamora, L. N., Darnley, J. A., Delisle, L., Hutson, K. S., Hills, J., & Geoghegan, J. L. (2025). A novel crustavirus as a candidate aetiology of tail fan necrosis in New Zealand red rock lobsters, Jasus edwardsii. Journal of Fish Diseases. Advance online publication. doi: 10.1111/jfd.70033
Grimwood, R. M., Darnley, J. A., O'Connell, J. P., Hunt, H., Taylor, H. S., Lawrence, K. E., … Geoghegan, J. L. (2025). Oral and faecal viromes of New Zealand calves on pasture with an idiopathic ill-thrift syndrome. Transboundary & Emerging Diseases, 2025, 7737989. doi: 10.1155/tbed/7737989
Hughes, H. R., Ballinger, M. J., Bao, Y., Bejerman, N., Blasdell, K. R., Briese, T., … Geoghegan, J. L., Grimwood, R. M., … ICTV Taxonomy Summary Consortium. (2025). Summary of taxonomy changes ratified by the International Committee on Taxonomy of Viruses (ICTV) from the Animal dsRNA and ssRNA(-) Viruses Subcommittee, 2025. Journal of General Virology, 106, 002112. doi: 10.1099/jgv.0.002112
Holdsworth, N. S., Weinzweig, N., Lalas, C., Waller, S. J., Geoghegan, J. L., & French, R. K. (2025). Uncovering the faecal virome of New Zealand sea lions (Phocarctos hookeri) reveals virus sharing among geographically distinct pinnipeds. Virology, 610, 110617. doi: 10.1016/j.virol.2025.110617
Waller, S. J., Niebuhr, C. N., Darnley, J. A., McInnes, K., Winter, D., Holmes, E. C., & Geoghegan, J. L. (2025). Metatranscriptomic detection of rabbit hemorrhagic disease virus 2 in karoro (southern black-backed gulls). Journal of Virology. Advance online publication. doi: 10.1128/jvi.00781-25
French, R. K., Waller, S. J., Wierenga, J. R., Grimwood, R. M., Hodgkinson-Bean, J., Digby, A., … French, N. P., & Geoghegan, J. L. (2025). Evidence for a role of extraintestinal pathogenic Escherichia coli, Enterococcus faecalis and Streptococcus gallolyticus in the aetiology of exudative cloacitis in the critically endangered Kākāpō (Strigops habroptilus). Molecular Ecology. Advance online publication. doi: 10.1111/mec.17761
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
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 acute respiratory illness associated with COVID-19 and influenza: Results of the SHIVERS II, III, IV prospective community cohort study. Journal of Infectious Diseases, 232(2), 450-464. doi: 10.1093/infdis/jiaf097
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, 101, fiaf016. doi: 10.1093/femsec/fiaf016
Hills, F. R., Geoghegan, J. L., & Bostina, M. (2025). Architects of infection: A structural overview of SARS-related coronavirus spike glycoproteins. Virology, 604, 110383. doi: 10.1016/j.virol.2024.110383
French, R. K., Anderson, S., Cain, K., Digby, A., Greene, T. C., Miskelly, C. M., … Geoghegan, J. L., & Holmes, E. C. (2025). Diversity and cross-species transmission of viruses in a remote island ecosystem: Implications for wildlife conservation. Virus Evolution, 11(1), veae113. doi: 10.1093/ve/veae113
Miller, A. K., Brosnahan, C. L., Pande, A., Baker, C. F., Geoghegan, J. L., Kitson, J., Gemmell, N. J., & Dowle, E. J. (2025). Formalin-fixed paraffin-embedded (FFPE) samples help to investigate transcriptomic responses in wildlife disease. Molecular Ecology Resources, 25, e13805. doi: 10.1111/1755-0998.13805
Journal - Research Other
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
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
Conference Contribution - Published proceedings: Abstract
Heremia, L., French, R., Waller, S. J., Wierenga, J., & Geoghegan, J. (2025). Uncovering virus diversity in urban waterfowl. Proceedings of the Infectious Diseases & Pandemic Preparedness Summit. (pp. 55). Retrieved from https://www.teniwha.com
Waller, S., & Geoghegan, J. (2025). Avian influenza virus surveillance across New Zealand and its subantarctic islands. Proceedings of the Infectious Diseases & Pandemic Preparedness Summit. (pp. 29). Retrieved from https://www.teniwha.com
Miller, A., Waller, S., Dowle, E., Winters, D., Besic, V., & Geoghegan, J. (2025). Environmental monitoring for avian influenza viruses in Aotearoa New Zealand. Proceedings of the 2nd Australian & New Zealand Environmental DNA (eDNA) Conference: eDNA Synergy: Innovate, Collaborate, Implement. Retrieved from https://ednaconference.com.au
2024
Journal - Research Article
Jelley, L., Aminisani, N., O'Neill, M., Jennings, T., Douglas, J., Utekar, S., … Welch, D., … SHIVERS Investigation Team, de Ligt, J., Winter, D., French, N., … Geoghegan, J. L. (2024). Tracing household transmission of SARS-CoV-2 in New Zealand using genomics. npj Viruses, 2, 21. doi: 10.1038/s44298-024-00032-6
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., … Nesdale, A., … Campbell-Stokes, P., … Geoghegan, J., de Ligt, J., Jelley, L., … Yu, C., … Baker, M. G., Kvalsvig, A., … Werno, 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
Geoghegan, J. (2024). Drivers of diversity in the virosphere [Plenary]. Proceedings of the 12th Australasian Virology Society (AVS) Meeting. Retrieved from https://www.avs.org.au
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)
Sweetman, E. C., Young, M. J., Schultz, H., & Geoghegan, J. L. (2024, September). Investigating the impact of fisheries on endangered hoiho diet, microbiome, and disease susceptibility. Poster session presented at the Queenstown Research Week (QRW) Pathogen Genomics Meeting, Queenstown, New Zealand.
Miller, A. K., Waller, S., Dowle, E., Winters, D., Besic, V., & Geoghegan, J. L. (2024, September). Environmental monitoring for avian influenza viruses in Aotearoa New Zealand. Poster session presented at the Queenstown Research Week (QRW) Pathogen Genomics Meeting, Queenstown, New Zealand.
Wierenga, J. R., Morgan, K. J., Hunter, S., Taylor, H., Argilla, L. S., Webster, T., Burga, L., Bostina, M., … Dubrulle, J., … Geoghegan, J. L. (2024, September). Genomics-informed diagnostics for infectious disease investigations in the endangered hoiho. Poster session presented at the Queenstown Research Week (QRW) Pathogen Genomics Meeting, Queenstown, New Zealand.
Taylor, J. T., Lee, V., Dearlove, T., Jolly, M., Wierenga, J. R., Dubrulle, J., Hodgkinson-Bean, J., … Geoghegan, J. L. (2024, September). A metagenomic investigation into Apteryx rowi dermatosis identifies multiple novel viruses and a highly abundant nematode. Poster session presented at the Queenstown Research Week (QRW) Pathogen Genomics Meeting, Queenstown, New Zealand.
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.
Heremia, L. R., French, R., Waller, S., Wierenga, J., & Geoghegan, J. L. (2024, September). Uncovering virus diversity in highly urbanised waterfowl. Poster session presented at the Queenstown Research Week (QRW) Pathogen Genomics Meeting, Queenstown, New Zealand.
de Vries, I. F., & Geoghegan, J. (2024, September). Virome seasonal dynamics of the New Zealand little neck clam, Austrovenus stutchburyi. Poster session presented at the Queenstown Research Week (QRW) Pathogen Genomics Meeting, Queenstown, New Zealand.
Scarlett-Herbert, E. Y., & Geoghegan, J. (2024, September). Four years of SARS-CoV-2 genomics in New Zealand. Poster session presented at the Queenstown Research Week (QRW) Pathogen Genomics Meeting, Queenstown, New Zealand.
Holdsworth, N., French, R., & Geoghegan, J. (2024, September). Revealing the virome of the New Zealand sea lion. Poster session presented at the Queenstown Research Week (QRW) Pathogen Genomics Meeting, Queenstown, New Zealand.
Grimwood, R. M., Waller, S. J., Wierenga, J. R., Lim, L., Dubrulle, J., Holmes, E. C., & Geoghegan, J. L. (2024, September). Viromes of Antarctic fish resembles the diversity found at lower latitudes. Poster session presented at the Queenstown Research Week (QRW) Pathogen Genomics Meeting, Queenstown, New Zealand.
Conference Contribution - Verbal presentation and other Conference outputs
French, R. K., Digby, A., Uddstrom, L., Eason, D., & Geoghegan, J. L. (2024, September). Comprehensive infectome analysis of an emerging disease in the critically endangered Kākāpō using total RNA sequencing. Verbal presentation at the Queenstown Research Week (QRW) Pathogen Genomics Meeting, Queenstown, New Zealand.
Waller, S. J., Wierenga, J., de Vries, I., Darnley, J., Taylor, J., Heremia, L., Dubrulle, J., Robinson, Z., … Geoghegan, J. L. (2024, September). Genomics-informed detection and surveillance to prepare Aotearoa for the existential threat of highly pathogenic avian influenza virus. Verbal presentation 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
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, July). The potential of genomics-informed pathogen diagnosis. Verbal presentation at the New Zealand Food Safety Science & Research Centre (NZFSSRC) Annual Symposium, Dunedin, New Zealand.
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.