Will Harvey CV

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Employment

2017–present. UKRI Innovation Fellow, Institute of Health and Wellbeing, 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 investigatorProf. 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 investigatorDr. Richard Reeve


Education

2011–2016 Ph.D. in Ecology and Evolutionary Biology, University of Glasgow.

ThesisQuantifying the genetic basis of antigenic variation among human influenza A viruses

SupervisorsDr. Richard ReeveProf. 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

SupervisorProf. 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).


Publications

2019

Davies, V., Harvey W.T., Reeve, R. and 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) DOI: 10.1111/rssc.12338

2018

Peacock T.P.*, Harvey W.T.*, Sadeyen J-R., Reeve, R. and Iqbal M. The molecular basis of antigenic variation among A(H9N2) avian influenza viruses. Emerging Microbes and Infections 7:176 *Authors contributed equally

2017

Goldstein, E.J., Harvey, W.T., Wilkie, G.S., Shepherd, S.J., MacLean, A.R., Murcia, P.R. and Gunson, R.N. Integrating patient and whole genome sequencing data to provide insights into the epidemiology of seasonal influenza A(H3N2) virusesMicrobial Genomics doi: 10.1099/mgen.0.000137

Davies, V., Reeve, R., Harvey W.T., Maree F.F. and Husmeier D. A sparse hierarchical Bayesian model for detecting relevant antigenic sites in virus evolution. Computational Statistics doi: 10.1007/s00180-017-0730-6

2016

Harvey, W.T., Benton D.J., Gregory, V., Hall, J.P.J., Daniels, R.S., Bedford, T., Haydon, D.T., Hay, A.J., McCauley, J.W. and 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 D.W.*, Maree F.F.*, Upadhyaya S., Lukhwareni A., Esterhuysen J.J., Harvey W.T., Blignaut B., Fry E.E., Parida S., Paton D.J. and Mahapatra M. Tracking the antigenic evolution of foot-and-mouth disease virus. PLoS ONE 11: e0159360 *Authors contributed equally

Davies V., Reeve R., Harvey W.T. and 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

2014

Davies V., Reeve R., Harvey W.T., Maree F.F. 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

2016-2019

Łuksza M., Harvey W.T., 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.

2016

Gregory V., Harvey W.T., Daniels R.S., Reeve R., Whittaker L., Halai C., Douglas A., Gonsalves R., Skehel J.J., Hay A.J. and McCauley J.W. 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


Professional Development

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. 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.


Technical skills

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)


Conference abstracts

2018

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.

2016

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.

2015

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.

2014

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.

2013

Identifying the proximate causes of antigenic evolution in influenza A. Epidemics4. 19–22 October. Amsterdam, Netherlands.


Invited Presentations

2019

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.

2014

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.