School of Biomedical Sciences

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