2022-present. Core Scientist, The Roslin Institute, University of Edinburgh.
2021-2022. Bioinformatician/Computational Biologist, MRC-University of Glasgow Centre for Virus Research, University of Glasgow.
2017–2021. UKRI Innovation Fellow, Institute of Health and Wellbeing/Institute of Biodiversity, Animal Health and Comparative Medicine, University of Glasgow.
Project: Using a comparative One Health approach to investigate the structural basis of antigenic variation among human and avian influenza viruses.
2016–2017. Postdoctoral Research Assistant, Institute of Biodiversity, Animal Health and Comparative Medicine, University of Glasgow.
Project: BBSRC and NSF funded project investigating the ecology and epidemiology of antimicrobial resistance at the human-animal interface in the Greater Serengeti Ecosystem.
Principal investigator: Prof. Louise Matthews
2016. Postdoctoral Research Assistant, Institute of Biodiversity, Animal Health and Comparative Medicine, University of Glasgow.
Project: University of Glasgow Knowledge Exchange Award to prepare and release the archive of data on human seasonal influenza H1N1 generated by the Worldwide Influenza Centre at the Francis Crick Institute
Principal investigator: Dr. Richard Reeve
2011–2016 Ph.D. in Ecology and Evolutionary Biology, University of Glasgow.
Thesis: Quantifying the genetic basis of antigenic variation among human influenza A viruses
Supervisors: Dr. Richard Reeve, Prof. John McCauley & Prof. Dan Haydon
2006–2010 B.Sc. (Hons) Biological Sciences (Evolutionary Biology) – First class, University of Edinburgh.
Dissertation: Investigating the cause of sex ratio bias in Drosophila miranda
Supervisor: Prof. Brian Charlesworth
Funding and Awards
MRC/BBSRC Skills Development Fellowship University of Glasgow (2017-2020).
British Council Newton Fund – Funded to present at the UK–Malaysia Vaccinology Workshop. Putrajaya, Malaysia (2016).
University of Glasgow Knowledge Exchange Award to prepare and release the archive of data on human seasonal influenza H1N1 generated by the Worldwide Influenza Centre at the Francis Crick Institute (2016).
BBSRC/British Council – Funded to present at the Food Security: Improving Approaches to Prevent and Control Viral Diseases of Livestock and Poultry workshop. Istanbul, Turkey (2015).
BBSRC Sparking Impact Award to fund running a symposium on viral phenotypes (2014).
David Searle Prize for academic writing (2013).
MRC Ph.D. Studentship University of Glasgow (2011-2015).
Harvey WT, Davies V, Daniels RS, Whittaker L, Gregory V, Hay AJ, Husmeier D, McCauley JW & Reeve R A Bayesian approach to incorporate structural data into the mapping of genotype to antigenic phenotype of influenza A(H3N2) viruses. bioRxiv DOI: 10.1101/2022.03.26.485931
Wright DW, Harvey WT, Hughes J, Cox M, Peacock TP, Colquhoun R, Jackson B, Orton R, Nielson M, Hsu NS, COVID-19 Genomics UK (COG-UK) Consortium, Harrison WM, de Silva TI, Rambaut A, Peacock SJ, Robertson DL & Carabelli AM Tracking SARS-CoV-2 mutations & variants through the COG-UK-Mutation Explorer. Virus Evolution veac023 DOI: 10.1093/ve/veac023
Willet BJ, Grove J, MacLean OA .. Harvey WT .. Robertson DL, Palmarini M, Ray S & Thomson EC The hyper-transmissible SARS-CoV-2 Omicron variant exhibits significant antigenic change, vaccine escape and a switch in cell entry mechanism. medRxiv https://doi.org/10.1101/2022.01.03.21268111
Forde TL, Dennis TPW, Aminu OR, Harvey WT, Hassim A, Kiwelu I, Medvecky M, Mshanga D, Van Heerden H, Vodel A, Zadoks RN, Mmbaga BT, Lembo T & Biek R Population genomics of Bacillus anthracis from an anthrax hyperendemic area reveals transmission processes across spatial scales and unexpected within-host diversity. Microbial Genomics 8, 000759 DOI: 10.1099/mgen.0.000759
Zhou J, Peacock TP, Brown JC, Goldhill DH, Elrefaey AME, Penrice-Randal R, Cowton VM, De Lorenzo G, Furnon W, Harvey WT, Kugathasan R, Frise R, Baillon L, Lassaunière R, Thakur N, Gallo G, Goldswain H, Donovan-Banfield I, Dong X, Randle NP, Sweeney F, Glynn MC, Quantrill JL, McKay PF, Patel AH, Palmarini M, Hiscox JA, Bailey D & Barclay WS Mutations that adapt SARS-CoV-2 to mink or ferrets do not increase fitness in the human airway. Cell Reports 38, 110344 DOI: 10.1016/j.celrep.2022.110344
Davis C, Logan N, Tyson G, Orton R, Harvey WT, Perkins J, Mollett G, Blacow RM, COVID-19 Genomics UK (COG-UK) Consortium, Peacock TP, Barclay WS, Cherepanov P, Palmarini M, Murcia PR, Patel AH, Robertson DL, Haughney J, Thomson EC & Willet BJ. (2021) Reduced neutralisation of the Delta (B.1.617.2) SARS-CoV-2 variant of concern following vaccination. PLOS Pathogens 17, e1010022
Meng B, Kemp SA, Papa G, Datir R, Ferriera IATM, Marelli S, Harvey WT, Lytras S, Mohamed A, Gallo G, Thakur N, Collier DA, MIcochova P, The COVID-19 Genomics UK (COG-UK) Consortium, Duncan LM, Carabelli AM, Kenyon JC, Lever AM, De Marco A, Saliba C, Culap K, Cameroni E, Matheson NJ, Piccoli L, Corti D, James LC, Robertson DL, Bailey D & Gupta RK (2021) Recurrent emergence of SARS-CoV-2 spike deletion H69/V70 and impact on B.1.1.7. Cell Reports 35, 109292 DOI: 10.1016/j.celrep.2021.209292
Harvey WT*, Carabelli AM*, Jackson B, Gupta RK, Thomson EC, Harrison EM, Ludden C, Reeve R, Rambaut A, COVID-19 Genomics UK (COG-UK) Consortium, Peacock SJ & Robertson DL SARS-CoV-2 variants, spike mutations and immune escape Nature Reviews Microbiology 19, 409-424. DOI: 10.1038/s41579-021-00573-0 *Joint first authors
Collier DA, De Marco A, Ferreira IATM, Meng B, Datir RP, Walls AC, Kemp SA, Bassi J, Pinto D, Silacci-Fregni C, Bianchi S, Tortorici MA, Bowen J, Culap K, Jaconi S, Cameroni E, Snell G, Pizzuto MS, Pellanda AF, Garzoni C, Riva A, The CITIID-NIHR BioResource COVID-19 Collaboration, Elmer A, Kingston N, Graves B, McCoy LE, Smith KGC, Bradley JR, Temperton N, Ceron-Gutierrez L, Barcenas-Morales G, The COVID-19 Genomics UK (COG-UK) Consortium, Harvey WT, Virgin HW, Lanzavecchia A, Piccoli L, Doffinger R, Wills M, Veesler D, Corti D & Gupta KR. Sensitivity of SARS-CoV-2 B.1.1.7 to mRNA vaccine-elicited antibodies. Nature 593, 136-141 DOI: 10.1038/s41586-021-03412-7
Peacock TP*, Sealy JE*, Harvey WT*, Benton DJ, Reeve R & Iqbal M. Genetic determinants of receptor-binding preference and zoonotic potential of H9N2 avian influenza viruses. Journal of Virology 95, e01651-20 DOI: 10.1101/2020.05.11.088 *Joint first authors
Scolamacchia F, Mulatti P, Mazzucato M, Barbujani M, Harvey WT, Fusaro A, Monne I, & Marangon S Different environmental gradients associated to the spatiotemporal and genetic pattern of the H5N8 highly pathogenic avian influenza outbreaks in poultry in Italy. Transboundary and Emerging Diseases 68, 152-167 doi: 10.1111/tbed.13661
Harvey WT, Mulatti P, Fusaro A, Scolamacchia F, Zecchin B, Monne I, & Marangon S Spatiotemporal reconstruction and transmission dynamics during the 2016-17 H5N8 highly pathogenic avian influenza epidemic in Italy. Transboundary and Emerging Diseases 68, 37-50 doi: 10.1111/tbed.13420
Kemp SA, Meng B, Ferriera IATM, Datir R, Harvey WT, Papa G, Lytras S, Collier DA, Mohamed A, Gallo G, Thakur N, The COVID-19 Genomics UK (COG-UK) Consortium, Carabelli AM, Kenyon JC, Lever AM, De Marco A, Saliba C, Culap K, Cameroni E, Piccoli L, Corti D, James LC, Bailey D, Robertson DL, Gupta RK. Recurrent emergence and transmission of a SARS-CoV-2 Spike deletion ΔH69/V70. bioRxiv doi: 10.1101/2020.12.14.422555
Maake L, Harvey WT, Rotherham L, Opperman PA, Theron J, Reeve R & Maree FF. Genetic basis of antigenic variation of SAT3 foot-and-mouth disease virus. Frontiers in Veterinary Science 7, 568 doi: 10.3389/fvets.2020.00568
Forde TL, Ratheesh NK, Harvey WT, Thomson JR, Williamson S, Biek R and Opriessnig T Genomic and immunogenic protein diversity of Erysipelothrix rhusiopathiae isolated from pigs in Great Britain: implications for vaccine protection. Frontiers in Microbiology 11:418 doi: 10.3389/fmicb.2020.00418
Davies V, Harvey WT, Reeve R & Husmeier D Improving the identification of antigenic sites in the H1N1 Influenza virus through accounting for the experimental structure in a sparse hierarchical Bayesian model. Journal of the Royal Statistical Society: Series C (Applied Statistics) 68, 859-885doi: 10.1111/rssc.12338
Peacock TP*, Harvey WT*, Sadeyen J-R, Reeve R & Iqbal M The molecular basis of antigenic variation among A(H9N2) avian influenza viruses. Emerging Microbes and Infections 7:176 doi: 10.1038/s41426-018-0178-y *Joint first authors
Goldstein EJ, Harvey WT, Wilkie GS, Shepherd SJ, MacLean AR, Murcia PR & Gunson RN Integrating patient and whole genome sequencing data to provide insights into the epidemiology of seasonal influenza A(H3N2) viruses. Microbial Genomics doi: 10.1099/mgen.0.000137
Davies V, Reeve R, Harvey WT, Maree FF & Husmeier D A sparse hierarchical Bayesian model for detecting relevant antigenic sites in virus evolution. Computational Statistics doi: 10.1007/s00180-017-0730-6
Harvey WT, Benton DJ, Gregory V, Hall JPJ, Daniels, RS, Bedford T, Haydon DT, Hay AJ, McCauley JW & Reeve R Identification of low- and high-impact hemagglutinin amino acid substitutions that drive antigenic drift of influenza A(H1N1) viruses. PLoS Pathogens 12: e1005526
Reeve R*, Borley DW*, Maree FF*, Upadhyaya S, Lukhwareni A, Esterhuysen JJ, Harvey WT, Blignaut B, Fry EE, Parida S, Paton DJ & Mahapatra M Tracking the antigenic evolution of foot-and-mouth disease virus. PLoS ONE 11: e0159360 *Authors contributed equally
Davies V, Reeve R, Harvey WT & Husmeier D Selecting random effect components in a sparse hierarchical Bayesian model for identifying antigenic variability. In: Computational Intelligence Methods for Bioinformatics and Biostatistics: 12th International Meeting, CIBB 2015, Naples, Italy, September 10-12, 2015, Revised Selected Papers. Series: Lecture Notes in Computer Science (9874). Springer, pp. 14-27. ISBN 9783319443317
Davies V, Reeve R, Harvey WT, Maree FF and Husmeier D Sparse Bayesian variable selection for the identification of antigenic variability in the foot-and-mouth disease virus. Journal of Machine Learning Research Workshop and Conference Proceedings 33: 149-158
Formal reports and data release
Łuksza M, Harvey WT, Reeve R, and Lässig M Formal reports detailing antigenic analyses and prediction of influenza A/H3N2 evolution contributed to biannual WHO Consultation and Information Meetings on the Composition of Influenza Virus Vaccines.
Gregory V, Harvey WT, Daniels RS, Reeve R, Whittaker L, Halai C, Douglas A, Gonsalves R, Skehel JJ, Hay AJ and McCauley JW Human former seasonal Influenza A(H1N1) haemagglutination inhibition data 1977–2009 from the WHO Collaborating Centre for Reference and Research on Influenza, London, UK. DOI: 10.5525/gla.researchdata.289
Organisation. Conceived and co-ordinated a one-day symposium with speakers from various institutes in Scotland and from overseas. Responsibilities, shared with a post-doctoral researcher, included formulating a programme of talks and contacting potential speakers, arranging a venue and accommodation, advertising the event and introducing speakers throughout the day. The 5th Boyd Orr Symposium: From viral genotype to phenotype.
Teaching. In 2019, I co-wrote and delivered a course on data visualisation using R and Shiny. The course has been run twice to researchers in Tanzania, at the Ifakara Health Institute, Bagamoyo and at the Nelson Mandela African Institute of Science and Technology, Arusha. During my Ph.D. I found acting as teaching assistant on the following courses to be extremely rewarding: Advanced Statistics (M.Sc. Quantitative Methods in Biodiversity, Conservation and Epidemiology, Level 4 undergraduate Zoology), Introduction to R (M.Sc. Quantitative methods.), Animal Physiology: Hypoxia in Carcinus (L3 Zoology), Data Analysis (L3 Animal Biology), Adh gene expression and Hardy-Weinberg equilibrium (L2 Evolutionary Biology).
Outreach. As a STEM ambassador (2013–present), I am enthusiastic participant in public engagement activities. This has included school visits and events within the Glasgow Science Festival. I’m a strong advocate of the benefits for the scientific community in actively engaging the next generation of scientists.
Quantitative techniques. Molecular phylogenetics, model testing using maximum-likelihood and Bayesian inference (GLM, GLMM, GAM, MCMC), descriptive methods of data analysis (e.g. MDS), epidemiological modelling, population genetics, antigenic cartography.
Laboratory. Mutagenesis, reverse genetics, cell culture, PCR, sequencing preparation and other standard techniques.
Programming and software. R, BUGS/JAGS, LaTeX, BEAST, HyPhy, PyMOL, Python (basic)
The influence of changes in antigenicity, avidity, and immunodominance on assays used for antigenic characterisation of influenza viruses. Influenza 2018: Centenary of the 1918 Symposium. 24–26 June. London, UK.
Using diversity analyses to examine the ecology of antibiotic resistance in closely linked human and livestock communities. British Ecological Society annual meeting. 11–14 May. Liverpool, UK.
Molecular markers of antigenic drift of avian and human influenza A viruses. UK–Malaysia Vaccinology Workshop. 1–4 August. Universiti Putra Malaysia, Malaysia.
Approaches for quantifying and predicting antigenic relationships among influenza A and FMD viruses. Food Security: Improving Approaches to Prevent and Control Viral Diseases of Livestock and Poultry. 12–15 May. Istanbul, Turkey.
Quantifying and predicting antigenic relationships: A comparison of two alternative approaches investigated using data from FMDV and influenza A. EuFMD. 29–31 October. Cavtat, Croatia.
Identifying the proximate causes of antigenic evolution in influenza A. Epidemics4. 19–22 October. Amsterdam, Netherlands.
UK-China BBSRC Newton Fund (Swine and Poultry) Workshop. The Pirbright Institute, Surrey, UK.
Invited Seminar. 12 June Instituto Zooprofilatico Sperimentale Veneto (IZSve), Legnaro, Italy.
Mini Symposium on Viral Evolution. 3–4 December. University of Cologne, Cologne, Germany.
The 19th Glasgow Virology Workshop. 1 February. MRC-University of Glasgow Centre for Virus Research, Glasgow, UK.
Conferences and meetings attended
The 1st UK Veterinary Vaccinology Network Conference. 16-17 February 2015. Birmingham, UK.
CIIE Symposium on Phylogeography of Human Pathogens. 7 February 2013. University of Edinburgh, Edinburgh, UK.
Next-generation Molecular and Evolutionary Epidemiology of Infectious Disease. 14-15 May 2012. The Royal Society, London, UK.