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.
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.
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 (http://www.otago.ac.nz/study/scholarships/index.html). A GPA of 7.5 or greater and demonstration of proficiency in English are essential.
Interested candidates with a BSc(Hons) or MSc degree are highly encouraged to get in touch.
Publications:
Grimwood RM, Fortune-Kelly G, Holmes EC, Ingram T, Geoghegan JL. 2023. Host specificity shapes fish viromes across lakes on an isolated remote island. Virology, 109884.
Bunce M, Geoghegan JL, Winter D et al. 2023. Exploring the depth and breadth of the genomics toolbox during the COVID-19 pandemic: insights from Aotearoa New Zealand. BMC Med 21, 213.
Miller AK, Brosnahan CL, Pande A, Baker CF, Geoghegan JL, Kitson J, Gemmell NJ, Dowle EJ. 2023. Formalin-fixed paraffin-embedded (FFPE) samples help to investigate transcriptomic responses in wildlife disease. Mol Ecol Resour, doi: 10.1111/1755-0998.13805.
JR Wierenga, KJ Morgan, S Hunter, HS Taylor, LS Argilla, T Webster, Dubrulle J, Jorge F, Bostina M, Burga L, Holmes EC, McInnes K, Geoghegan JL. 2023. A novel gyrovirus is abundant in yellow-eyed penguin (Megadyptes antipodes) chicks with a fatal respiratory disease. Virology (in press).
Costa VA, Bellwood DR, Mifsud JCO, Van Brussel K, Geoghegan JL, Holmes EC, Harvey E. 2023. Limited cross-species virus transmission in a spatially restricted coral reef fish community. Virus Evolution, vead011.
Van Brussel K, Mahar JE, Ortiz-Baez AS, Carrai M, Spielman D, Boardman WSJ, Baker ML, Beatty JA, Geoghegan JL, Barrs VR, Holmes EC. 2022. Faecal virome of the Australian grey-headed flying fox from urban/suburban environments contains novel coronaviruses, retroviruses and sapoviruses. Virology, 576, 42-51.
J Douglas, D Winter, A McNeill, S Carr, M Bunce, N French, J Hadfield, de Ligt J, Welch D, Geoghegan JL. 2022. Tracing the international arrivals of SARS-CoV-2 Omicron variants after Aotearoa New Zealand reopened its border. Nature Communications, 13 (1), 6484.
VA Costa, JL Geoghegan, EC Holmes, E Harvey. 2022. Genetic Reassortment between Endemic and Introduced Macrobrachium rosenbergii Nodaviruses in the Murray-Darling Basin, Australia. Viruses, 14 (10), 2186.
Waller SJ, Lamar S, Perry BJ, Grimwood RM, Holmes EC, Geoghegan JL. 2022. Cloacal virome of an ancient host lineage – the tuatara (Sphenodon punctatus) – reveals abundant and diverse diet-related viruses. Virology, 575, 43-53.
Jelley L, Douglas J, Ren X, Winter D, McNeill A, Huang S, French N, Welch D, Hadfield J, de Ligt J, Geoghegan JL. 2022.Genomic epidemiology of Delta SARS-CoV-2 during transition from elimination to suppression in Aotearoa New Zealand. Nature Communications (in press).
Fox-Lewis A, Williamson F, Harrower J, Ren X, Sonder GJB, McNeill A, de Ligt J, Geoghegan JL. 2022. Airborne transmission of SARS-CoV-2 Delta variant within a tightly monitored isolation facility, New Zealand (Aotearoa). Emerging Infectious Disease, 28(3).
Perry BJ, Darestani MM, Ara MG, Hoste A, Jandt JM, Dutoit L, Holmes EC, Ingram T, Geoghegan JL. 2022. Viromes of freshwater fish with lacustrine and diadromous life histories differ in composition. Viruses, 14(2).
Mifsud JCO, Gallagher RV, Holmes EC, Geoghegan JL. 2022. Transcriptome mining reveals a spectrum of RNA viruses in primitive plants. Journal of Virology (in press).
Holmes EC, Goldstein SA, Rasmussen AL, Robertson DL, Crits-Christoph A, Wertheim JO, Anthony SJ, Barclay WS, Boni MF, Doherty PC, Farrer J, Geoghegan JL, Jiang X, et al. 2021. The origins of SARS-CoV-2: a critical review. Cell 184(19), 4848-4856.
Nguyen T, Adnan M, Nguyen BP, de Ligt J, Geoghegan JL, Dean R, et al. 2021. COVID-19 vaccine strategies for Aotearoa New Zealand: a mathematical modelling study. The Lancet Regional Health – Western Pacific (in press).
Douglas J, Geoghegan JL, Hadfield J, Bouckaert R, Storey M, Ren X, de Ligt J, French N, Welch D. 2021. Real-time genomics to track COVID-19 post-elimination border incursions in Aotearoa New Zealand. Emerging Infectious Disease (in press).
Douglas J, Mendes FK, Bouckaert R, Xie D, Jimenez-Silva CL, Swanepoel C, de Ligt J, Ren X, Storey M, Hadfield J, Simpson CR, Geoghegan JL, Welch D, Drummond AJ. 2021. Phylodynamics reveals the role of human travel and contact tracing in controlling COVID-19 in four island nations. Virus Evolution (in press).
Miller AK, Mifsud JCO, Costa VA, Grimwood RM, Kitson J, Baker C, Brosnahan CL, Pande A, Holmes EC, Gemmell NJ, Geoghegan JL. 2021. Slippery when wet: cross-species transmission of divergent coronaviruses in bony and jawless fish and the evolutionary history of the Coronaviridae. Virus Evolution (in press).
O'Toole Á, Hill V, Pybus OG, ... Geoghegan JL et al. 2021. Tracking the international spread of SARS-CoV-2 lineages B.1.1.7 and B.1.351/501Y-V2. Wellcome Open Res, 6:121.
Wille M, Geoghegan JL, EC Holmes. 2021. How accurately can we predict pandemic risk? PLoS Biology, 19(4): e3001135.
VA Costa, JCO Mifsud, D Gilligan, JE Williamson, EC Holmes, Geoghegan JL. 2021. Metagenomic sequencing reveals a lack of virus exchange between native and invasive freshwater fish across the Murray-Darling Basin, Australia. Virus Evolution, veab034.
Nielsen DA, Fierer N, Geoghegan JL, Gillings MR, Gumerov V, Madin JS, Moore L, Paulsen IT, Reddy TBK, Tetu SG, Westoby M. 2021. Aerobic bacteria and archaea tend to have large and more versatile genomes. Oikos, 4, 130.
Sanjuán R, Illingworth C, Geoghegan JL, Iranzo J, Zwart M, Ciota A, Moratorio G, Gago-Zachert S, Duffy S, Vijaykrishna D. 2021. Five challenges in the field of viral diversity and evolution. Frontiers in Virology, 1, 1-4.
Grimwood RM, Holmes EC, Geoghegan JL. 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.
Eichler N, Thornley C, Swadi T, Devine T, McElnay C, Sherwood J, Brunton C, Williamson F, Freeman J, Berger S, Ren X, Storey M, de Ligt J, Geoghegan JL. 2021. Transmission of SARS-CoC-2 during border quarantine and air travel in Aotearoa New Zealand. Emerging Infectious Disease, 27(5).
Geoghegan JL, Moreland NJ, Le Gros G, Ussher JE. 2021. New Zealand’s science-led response to the SARS-CoV-2 pandemic. Nature Immunology, 22, 262-263.
Geoghegan JL, Douglas J, Ren X, Storey M, Hadfield J, Silander OK, Freed NE, Jelley L, Jefferies S, Sherwood J, Paine S, Huang S, Sporle A, Baker MG, Murdoch DR, Drummond AJ, Welch D, Simpson CR, French N, Holmes EC, de Ligt J. 2021. Use of genomics to track coronavirus disease outbreaks, New Zealand. Emerging Infectious Diseases, 27(5), 1317.
Geoghegan JL, Di Giallonardo F, Wille M, Ortiz-Baez AS, Costa VA, Ghaly T, Mifsud JCO, Turnbull OMH, Bellwood DR, Williamson JE, Holmes EC. 2021. Virome composition in marine fish revealed by meta-transcriptomics. Virus Evolution, veab005.
Swadi T*, Geoghegan JL* (Joint first author), Devine T, McElnay C, Sherwood J, Shoemack P, Ren X, Storey M, Jefferies S, Smit E, Hadfield J, Kenny A, Jelley L, Sporle A, McNeill A, Reynolds GE, Mouldey K, Lowe L, Sonder G, Drummond AJ, Huang S, Welch D, Holmes EC, French N, Simpson C, de Ligt J. 2021. Genomic evidence supports in-flight transmission of SARS-CoV-2 despite pre-departure testing. Emerging Infectious Diseases, 27(3).
Di Giallonardo F, Pinto AN, Keen P, Shaik A, Carrera A, Salem H, Selvey C, Nigro SJ, Fraser N, Price K, Holden J, Lee FJ, Dwyer DE, Bavinton BJ, Geoghegan JL, Grulich AE, Kelleher AD, on behalf of the NSW HIV Prevention Partnership Project. 2021. 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, 24(1):e25655.
Geoghegan JL, Ren X, Storey M, Hadfield J, Jelley L, Jefferies S, Sherwood J, Paine S, Huang S, Douglas J, Mendes FK, Sporle A, Baker MG, Murdoch DR, French N, Simpson CR, Welch D, Drummond AJ, Holmes EC, Duchene S, de Ligt J. 2020. Genomic epidemiology reveals transmission patterns and dynamics of SARS-CoV-2 in Aotearoa New Zealand. Nature Communications, 11, 6351.
Turnbull OMH, Ortiz-Baez AS, Eden JS, Shi M, Williamson JE, Gaston TF, Zhang YZ, Holmes EC, Geoghegan JL. 2020. Meta-transcriptomic identification of divergent Amnoonviridae in fish. Viruses, 12(11), 1254.
Parry R, Wille M, Turnbull OMH, Geoghegan JL, Holmes EC. 2020. Divergent influenza-like viruses of amphibians and fish support an ancient evolutionary association. Viruses, 12(9), 1042.
Campbell SJ, Ashley W, Gil-Fernandez M, Newsome TM, Di Giallonardo F, Ortiz-Baez AS, Mahar JE, Towerton AL, Gillings M, Holmes EC, Carthey AJR, Geoghegan JL. 2020. Red fox viromes in urban and rural landscapes. Virus Evolution, 6(2), veaa065.
Madin J, Nielsen D, Brbic M, Corkrey R, Danko D, Edwards K, Engqvist M, Fierer N, Geoghegan JL, Gillings M, Kyrpides N, Litchman E, Mason C, Moore L, Nielsen S, Paulsen I, Price N, Reddy T, Richards M, Rocha E, Schmidt T, Shaaban H, Shukla M, Supek F, Tetu S, Vieira-Silva S, Wattam A, Westfall D, Westoby M. 2020. A synthesis of bacterial and archaeal phenotypic trait data. Scientific Data. 7 (1), 1-8.
Ghaly TM, Geoghegan JL, Tetu SG Gillings MR. 2020. The peril and promise of integrons: beyond antibiotic resistance. Trends in Microbiology. 28 (6), 455-464.
Ghaly TM, Geoghegan JL, Alroy J, Gillings MR. 2019. High diversity and rapid spatial turnover of integron gene cassettes in soil. Environmental Microbiology. 21(5).
Geoghegan JL, Holmes EC. 2018. The phylogenomics of evolving virus virulence. Nature Reviews Genetics, 1.
Geoghegan JL, Holmes EC. 2018. Evolutionary virology at 40. Genetics, 210(4), 1151-1162.
Geoghegan JL, Di Giallonardo F, Cousins K, Shi M, Williamson JE, Holmes EC. 2018. Hidden diversity and evolution in market fish. Virus Evolution, 4(2).
Di Giallonardo F, Kok J, Fernandez M, Carter I, Geoghegan JL, Dwyer D, Holmes EC, Eden JS. 2018. Evolution of human respiratory syncytial virus (RSV) over multiple seasons in New South Wales, Australia. Viruses, 10(9): 476.
Geoghegan JL, Pirotta V, Harvey E, Smith A, Buchmann JP, Ostrowski M, Eden JS, Harcourt R, Holmes EC. 2018. Virological sampling of inaccessible wildlife with drones. Viruses, 10(6): 300.
Geoghegan JL, Saavedra AF, Duchêne S, Sullivan S, Barr I, Holmes EC. 2018. Continental synchronicity of human influenza virus epidemics despite climatic variation. PLoS Pathogens. 14(1), e1006780.
Tong JK, Duchêne DA, Duchêne S, Geoghegan JL, Ho SYW. 2018. A comparison of methods for estimating substitution rates from ancient DNA sequence data. BMC Evolutionary Biology. 18(1): 70.
Duchêne S, Duchêne DA, Geoghegan JL, Dyson ZA, Hawkey J, Holt KE. 2018. Inferring demographic parameters in bacterial genomic data using Bayesian and hybrid phylogenetic methods. BMC Evolutionary Biology. 18(95)
Geoghegan JL, Holmes EC. 2017. Predicting virus emergence amidst evolutionary noise. Open Biology. 7 (10), 170189.
Geoghegan JL, Duchêne S, Holmes EC. 2017. Comparative analysis estimates the relative frequencies of co-divergence and cross-species transmission within viral families. PLoS Pathogens. 13(2): e1006215.
Geoghegan JL, Senior AM, Di Giallonardo F, Holmes EC. 2016. Virological factors that increase the transmissibility of emerging human viruses. Proceedings of the National Academy of Sciences USA. 113(15): 4170-4175.
Geoghegan JL, Senior AM, Holmes EC. 2016. Pathogen population bottlenecks and adaptive landscapes: overcoming the barriers to disease emergence. Proceedings of the Royal Society of London B. 283(1837): 20160727.
Duchêne S*, Geoghegan JL* (Joint first author), Holmes EC, Ho SYW. 2016. Estimating evolutionary rates using time-structured data: a general comparison of phylogenetic methods. Bioinformatics. 1-5.
Di Giallonardo F, Geoghegan JL, Docherty DE, McLean RG, Zody MC, Qu J, Yang X, Birren BW, Malboeuf CM, Newman RM, Ip HS, Holmes EC. 2016. Fluid spatial dynamics of West Nile virus in the USA: rapid spread in a permissive host environment. Journal of Virology. 90(2): 862-872.
Duchêne S, Duchêne DA, Di Giallonardo F, Eden JS, Geoghegan JL, Holt KE, Ho SYW, Holmes EC. 2016. Cross-validation to select Bayesian hierarchical models in phylogenetics. BMC Evolutionary Biology. 16(115).
Geoghegan JL, Tan le V, Kühnert D, Halpin RA, Lin X, Simenauer A, Akopov A, Das SR, Stockwell TB, Shrivastava S, Ngoc NM, Uyen le TT, Tuyen NT, Thanh TT, Hang VT, Qui PT, Hung NT, Khanh TH, Thinh le Q, Nhan le NT, Van HM, Viet do C, Tuan HM, Viet HL, Hien TT, Chau NV, Thwaites G, Grenfell BT, Stadler T, Wentworth DE, Holmes EC, Van Doorn HR. 2015. Phylodynamics of enterovirus A71-associated hand, foot and mouth disease in Viet Nam. Journal of Virology. 89(17): 8871-8879.
Tan le V, Tuyen NT, Thanh TT, Ngan TT, Van HM, Sabanathan S, Van TT, Thanh le TM, Nguyet LA, Geoghegan JL, Ong KC, Perera D, Hang VT, Ny NT, Anh NT, Ha do Q, Qui PT, Viet do C, Tuan HM, Wong KT, Holmes EC, Chau NV, Thwaites G, van Doorn HR. 2015. A generic assay for whole-genome amplification and deep sequencing of enterovirus A71. Journal of Virological Methods. 215: 30-36.
Lopes AM, Capucci L, Gavier-Widén D, Le Gall-Reculé G, Brocchi E, Barbieri I, Quéméner A, Le Pendu J, Geoghegan JL, Holmes EC, Esteves PJ, Abrantes J. 2014. Molecular evolution and antigenic variation of European brown hare syndrome virus (EBHSV). Virology. 468: 104-112.
Geoghegan JL, Walker PJ, Duchemin JB, Jeanne I, Holmes EC. 2014. Seasonal drivers of the epidemiology of arthropod-borne viruses in Australia. PLoS Neglected Tropical Diseases. 8(11): e3325.
Dalziel BD, Huang, K Geoghegan JL, Arinaminpathy N, Dubovi EJ, Grenfell BT, Ellner SP, Holmes EC, Parrish CR. 2014. Contact heterogeneity, rather than transmission efficiency, limits the emergence and spread of canine influenza virus. PLoS Pathogens. 10(10): e1004455.
Geoghegan JL, Spencer HG. 2013. The adaptive invasion of epialleles in a heterogeneous environment. Theoretical Population Biology. 88: 1-8.
Geoghegan JL, Spencer HG. 2013. The evolutionary potential of paramutation: A population-epigenetic model. Theoretical Population Biology. 88: 9-19.
Geoghegan JL, Spencer HG. 2012. Exploring epiallele stability in a population-epigenetic model. Theoretical Population Biology. 83: 136–144.
Geoghegan JL, Spencer HG. 2012. Population-epigenetic models of selection. Theoretical Population Biology. 81(3): 232-242.
Book chapters:
Geoghegan JL, Holmes EC. 2020. Chapter 1: Virus Evolution. Fields Virology, Emerging Viruses.
Geoghegan JL. 2014. Transgenerational epigenetics (edited by Trygve Tollefsbol). Chapter 15: Inheritance of epigenome variants across generations and its implications on the emergence of phenotypic novelties during evolution. Elsevier.
