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Microbiology Logo Microbiology & Immunology
Te Tari Moromoroiti me te Ārai Mate

Dr Jemma Geoghegan

Current research:

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 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. 



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. medRxiv, doi: 

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. 2020. Phylodynamics reveals the role of human travel and contact tracing in controlling COVID-19 in four island nations. medRxiv, doi:

Geoghegan JL, Di Giallonardo F, Wille M, Ortiz-Baez AS, Costa VA, Ghaly T, Mifsud JCO, Turnbull OMH, Bellwood DR, Williamson JE, Holmes EC. 2020. Host evolutionary history and ecology shape virome composition in fishes. bioRxiv, doi:

Wille M, Geoghegan JL, Holmes EC. 2020. How accurately can we assess zoonotic risk? bioRxiv, doi: 

Parry R, Wille M, Turnbull O, Geoghegan JL, Holmes EC. 2020. Divergent influenza-like viruses of amphibians and fish support an ancient evolutionary association. Viruses, in press. 

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, in press.

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.