Preprints

Steyn, N., & Parag, K. V. (2025). Robust uncertainty quantification in popular estimators of the instantaneous reproduction number. medRxiv preprint. https://doi.org/10.1101/2024.10.22.24315918

Steyn, N., Parag, K. V., Thompson, R. N., & Donnelly, C. A. (2025). A primer on inference and prediction with epidemic renewal models using sequential Monte Carlo methods. arXiv preprint. https://doi.org/10.48550/arXiv.2503.18875

Steyn, N., Chadeau-Hyam, M., Elliott, P., & Donnelly, C. A. (2025). Bayesian modelling of repeated cross-sectional epidemic prevalence survey data. medRxiv preprint. https://doi.org/10.1101/2025.04.16.25325936

Steyn, N., Unwin, H. J. T., Ponmattam, J., et al. (2025). Regional and national estimates of children affected by all-cause and COVID-19-associated orphanhood and caregiver death in Brazil, by age and family circumstance. medRxiv preprint. https://doi.org/10.1101/2025.01.31.25321479

Steyn, N., Chadeau-Hyam, M., Whitaker, M., et al. (2025). Pandemic-risk-related behaviour change in England from June 2020 to March 2022: REACT-1 study among over 2 million people. medRxiv preprint. https://doi.org/10.1101/2025.03.03.25323250

Online resources

SMC and epidemic renewal models: an online “book” demonstrating sequential Monte Carlo methods for fitting epidemic renewal models. Accompanies A primer on inference and prediction with epidemic renewal models using sequential Monte Carlo methods.

Rt estimators in Julia: short vignettes accompanying the code provided in the GitHub repository for Robust uncertainty quantification in popular estimators of the instantaneous reproduction number. Provides Julia implementation of EpiEstim and EpiFilter, as well as the corresponding parameter fitting methodology developed in the paper.

Pandemic-risk-related behavioural data portal: an R shiny server hosting a large quantity of aggregated data on pandemic-risk-related behaviours in England, collected as part of the REACT-1 study. By making these data publicly available, we hope to enable further research. Methodology can be found in our preprint.

Posters

Presented at IDM 2024. Download here.

Presented at IDM 2024. Download here.

Presented at EPIDEMICS 2023. Download here.

Presented at EPIDEMICS 2023. Download here.

Publications

2025

Ogi-Gittins, I., Steyn, N., Polonsky, J., Hart, W. S., Keita, M., Ahuka-Mundeke, S., Hill, E. M., & Thompson, R. N. (2025). Simulation-based inference of the time-dependent reproduction number from temporally aggregated and under-reported disease incidence time series data. Philosophical Transactions of the Royal Society A. http://doi.org/10.1098/rsta.2024.0412

2024

Watson, L. M., Plank, M. J., Armstrong, B. A., Chapman, J. R., Hewitt, J., Morris, H., Orsi, A., Bunce, M., Donnelly, C. A., & Steyn, N. (2024). Jointly estimating epidemiological dynamics of Covid-19 from case and wastewater data in Aotearoa New Zealand. Communications Medicine. https://doi.org/10.1038/s43856-024-00570-3

2023

Binny, R. N., Priest, P., French, N. P., Parry, M., Lustig, A., Hendy, S. C., Maclaren, O. J., Ridings, K. M., Steyn, N., Vattiato, G., & Plank, M. J. (2023). Sensitivity of Reverse Transcription Polymerase Chain Reaction Tests for Severe Acute Respiratory Syndrome Coronavirus 2 Through Time. The Journal of Infectious Diseases. https://doi.org/10.1093/infdis/jiac317

Elliott, P., Whitaker, M., Tang, D., Eales, O., Steyn, N., Bodinier, B., Wang, H., Elliott, J., Atchison, C., Ashby, D., Barclay, W., Taylor, G., Darzi, A., Cooke, G. S., Ward, H., Donnelly, C. A., Riley, S., & Chadeau-Hyam, M. (2023). Design and Implementation of a National SARS-CoV-2 Monitoring Program in England: REACT-1 Study. American Journal of Public Health. https://doi.org/10.2105/AJPH.2023.307230

2022

Elliott, P., Eales, O., Steyn, N., Tang, D., Bodinier, B., Wang, H., Elliott, J., Whitaker, M., Atchison, C., Diggle, P. J., Page, A. J., Trotter, A. J., Ashby, D., Barclay, W., Taylor, G., Ward, H., Darzi, A., Cooke, G. S., Donnelly, C. A., & Chadeau-Hyam, M. (2022). Twin peaks: the Omicron SARS-CoV-2 BA. 1 and BA. 2 epidemics in England. Science. https://doi.org/10.1126/science.abq4411

Plank, M. J., James, A., Lustig, A., Steyn, N., Binny, R. N., & Hendy, S. C. (2022). Potential reduction in transmission of COVID-19 by digital contact tracing systems: a modelling study. Mathematical Medicine and Biology. https://doi.org/10.1093/imammb/dqac002

Steyn, N., Lustig, A., Hendy, S. C., Binny, R. N., & Plank, M. J. (2022). Effect of vaccination, border testing, and quarantine requirements on the risk of COVID-19 in New Zealand: A modelling study. Infectious Disease Modelling. https://doi.org/10.1016/j.idm.2021.12.006

Steyn, N., Plank, M. J., Binny, R. N., Hendy, S. C., Lustig, A., & Ridings, K. (2022). A COVID-19 vaccination model for Aotearoa New Zealand. Scientific Reports https://doi.org/10.1038/s41598-022-06707-5

2021

Hendy, S., Steyn, N., James, A., Plank, M. J., Hannah, K., Binny, R. N., & Lustig, A. (2021). Mathematical modelling to inform New Zealand’s COVID-19 response. Journal of the Royal Society of New Zealand. https://doi.org/10.1080/03036758.2021.1876111

James, A., Plank, M. J., Hendy, S., Binny, R., Lustig, A., Steyn, N., Nesdale, A., & Verrall, A. (2021). Successful contact tracing systems for COVID-19 rely on effective quarantine and isolation. PLoS One. https://doi.org/10.1371/journal.pone.0252499

Steyn, N., Binny, R. N., Hannah, K., Hendy, S., James, A., Lustig, A., Ridings, K., Plank, M. J., & Sporle, A. (2021). Māori and Pacific People in New Zealand have higher risk of hospitalisation for COVID-19. New Zealand Medical Journal. Link to PDF

James, A., Plank, M. J., Binny, R. N., Lustig, A., Hannah, K., Hendy, S. C., & Steyn, N. (2021). A structured model for COVID-19 spread: modelling age and healthcare inequities. Mathematical Medicine and Biology. https://doi.org/10.1093/imammb/dqab006

Binny, R. N., Baker, M. G., Hendy, S. C., James, A., Lustig, A., Plank, M. J., Ridings, K. M., & Steyn, N. (2021). Early intervention is the key to success in COVID-19 control. Royal Society Open Science. https://doi.org/10.1098/rsos.210488

Steyn, N., Plank, M. J., James, A., Binny, R. N., Hendy, S. C., & Lustig, A. (2021). Managing the risk of a COVID-19 outbreak from border arrivals. Journal of the Royal Society Interface. https://doi.org/10.1098/rsif.2021.0063

Plank, M., James, A., & Steyn, N. (2021). Comment: weekly COVID-19 testing with household quarantine and contact tracing is feasible and would probably end the epidemic1. Royal Society Open Science. https://doi.org/10.1098/rsos.201546

James, A., Plank, M. J., Hendy, S., Binny, R. N., Lustig, A., & Steyn, N. (2021). Model-free estimation of COVID-19 transmission dynamics from a complete outbreak. PLOS ONE. https://doi.org/10.1371/journal.pone.0238800

2020

Steyn, N., Binny, R. N., Hannah, K., Hendy, S., James, A., Kukutai, T., Lustig, A., McLeod, M., Plank, M. J., Ridings, K., & Sporle, A. (2020). Estimated inequities in COVID-19 infection fatality rates by ethnicity for Aotearoa New Zealand. New Zealand Medical Journal. Link to PDF

Technical reports

Steyn, N., Plank, M. J., & Hendy, S. C. (2021). Modelling to support a future COVID-19 strategy for Aotearoa New Zealand. Link to PDF

Steyn, N., Hendy, S., Plank, M., & Binny, R. (2021). Technical report: modelling the potential spread of COVID-19 during the August 2021 outbreak. Link to PDF

James, A., Binny, R. N., Hendy, S. C., Lustig, A., Steyn, N., & Plank, M. J. (2020). Economic comparison of the use of Alert Levels 3 and 4 in eliminating the Auckland August outbreak: a cost-effectiveness analysis 21 October 2020. Link to PDF

Binny, R. N., Hendy, S. C., James, A., Lustig, A., Plank, M. J., & Steyn, N. (2020). Probability of elimination for COVID-19 in Aotearoa New Zealand. https://doi.org/10.1101/2020.08.10.20172361

Binny, R. N., Lustig, A., Brower, A., Hendy, S. C., James, A., Parry, M., Plank, M. J., & Steyn, N. (2020). Effective reproduction number for COVID-19 in Aotearoa New Zealand. https://doi.org/10.1101/2020.08.10.20172320

Binny, R. N., Hendy, S. C., James, A., Lustig, A., Plank, M. J., & Steyn, N. (2020). Effect of Alert Level 4 on Reff: review of international COVID-19 cases. https://doi.org/10.1101/2020.04.30.20086934

Plank, M. J., Binny, R. N., Hendy, S. C., Lustig, A., James, A., & Steyn, N. (2020). A stochastic model for COVID-19 spread and the effects of Alert Level 4 in Aotearoa New Zealand. https://doi.org/10.1101/2020.04.08.20058743

James, A., Hendy, S. C., Plank, M. J., & Steyn, N. (2020). Suppression and mitigation strategies for control of COVID-19 in New Zealand. https://doi.org/10.1101/2020.03.26.20044677

Media

Steyn, N., & Plank, M. J. Why strict border control remains crucial if we want to keep the travel bubble safe. The Conversation. 21 April 2021. Link

Plank, M. J., James, A., Steyn, N., & Hendy, S. C. Auckland’s rapid lockdown has given New Zealand a better chance of eliminating coronavirus – again. The Conversation. 28 August 2020. Link

Steyn, N., Plank, M. J., James, A., Binny, R. N., Lustig, A., & Hendy, S. C. A critical error in a report on lockdown timing risks undermining future decisions. The Spinoff. 10 August 2020. Link

Plank, M. J., James, A., Lustig, A., Steyn, N., Binny, R. N., & Hendy, S. C. A new community case of COVID-19 in New Zealand is a matter of when, not if. Is the country prepared for it? The Conversation. 10 August 2020. Link

Plank, M. J., James, A., Lustig, A., Steyn, N., Binny, R. N., & Hendy, S. C. How New Zealand could keep eliminating coronavirus at its border for months to come, even as the global pandemic worsens. The Conversation. 16 July 2020. Link

Plank, M. J., James, A., Lustig, A., Steyn, N., Binny, R. N., & Hendy, S. C. 2 new COVID-19 cases in New Zealand, but elimination of community transmission still stands. The Conversation. 16 June 2020. Link

Plank, M. J., James, A., Lustig, A., Steyn, N., Binny, R. N., & Hendy, S. C. New Zealand hits a 95% chance of eliminating coronavirus – but we predict new cases will emerge. The Conversation. 4 June 2020. Link

Awards

Prime Minister’s Science Prize. 2020. Awarded for a “transformative scientific discovery or achievement” with a significant impact on New Zealand. This was awarded for our work on modelling during the COVID-19 pandemic in New Zealand.

Footnotes

  1. This is a published comment piece on a paper arguing that household quarantine and contact tracing would have been sufficient to end the pandemic. We were arguing that it would not have been sufficient.↩︎