Deterministic epidemic models overestimate the basic reproduction number of observed outbreaks

no code implementations • 13 Apr 2023 • Wajid Ali, Christopher E. Overton, Robert R. Wilkinson, Kieran J. Sharkey

The basic reproduction number, $R_0$, is a well-known quantifier of epidemic spread.

Nowcasting the 2022 mpox outbreak in England

1 code implementation • 17 Feb 2023 • Christopher E. Overton, Sam Abbott, Rachel Christie, Fergus Cumming, Julie Day, Owen Jones, Rob Paton, Charlie Turner, Thomas Ward

In May 2022, a cluster of mpox cases were detected in the UK that could not be traced to recent travel history from an endemic region.

Additive models

Approximating quasi-stationary behaviour in network-based SIS dynamics

no code implementations • 11 Aug 2022 • Christopher E. Overton, Robert R. Wilkinson, Adedapo Loyinmi, Joel C. Miller, Kieran J. Sharkey

Here we relate the approximate models to the stochastic dynamics via the definition of the quasi-stationary distribution (QSD), which captures this approximately stable behaviour.

Novel methods for estimating the instantaneous and overall COVID-19 case fatality risk among care home residents in England

1 code implementation • 15 Feb 2022 • Christopher E. Overton, Luke Webb, Uma Datta, Mike Fursman, Jo Hardstaff, Iina Hiironen, Karthik Paranthaman, Heather Riley, James Sedgwick, Julia Verne, Steve Willner, Lorenzo Pellis, Ian Hall

To estimate CFR, we apply both novel and existing methods to data on deaths in care homes, collected by Public Health England and the Care Quality Commission.

EpiBeds: Data informed modelling of the COVID-19 hospital burden in England

no code implementations • 12 Oct 2021 • Christopher E. Overton, Lorenzo Pellis, Helena B. Stage, Francesca Scarabel, Joshua Burton, Christophe Fraser, Ian Hall, Thomas A. House, Chris Jewell, Anel Nurtay, Filippo Pagani, Katrina A. Lythgoe

In order to predict the effect of the local epidemic on hospital capacity in England, we used a variety of data streams to inform the construction and parameterisation of a hospital progression model, which was coupled to a model of the generalised epidemic.

Evolutionary graph theory derived from eco-evolutionary dynamics

no code implementations • 30 Oct 2020 • Karan Pattni, Christopher E. Overton, Kieran J. Sharkey

For example, the star network, which is known to be an amplifier of selection in evolutionary graph theory, can inhibit the spread of adaptive mutations when individuals can die naturally.

Using statistics and mathematical modelling to understand infectious disease outbreaks: COVID-19 as an example

1 code implementation • 11 May 2020 • Christopher E. Overton, Helena B. Stage, Shazaad Ahmad, Jacob Curran-Sebastian, Paul Dark, Rajenki Das, Elizabeth Fearon, Timothy Felton, Martyn Fyles, Nick Gent, Ian Hall, Thomas House, Hugo Lewkowicz, Xiaoxi Pang, Lorenzo Pellis, Robert Sawko, Andrew Ustianowski, Bindu Vekaria, Luke Webb

During an infectious disease outbreak, biases in the data and complexities of the underlying dynamics pose significant challenges in mathematically modelling the outbreak and designing policy.

Populations and Evolution Physics and Society

Challenges in control of Covid-19: short doubling time and long delay to effect of interventions

1 code implementation • 31 Mar 2020 • Lorenzo Pellis, Francesca Scarabel, Helena B. Stage, Christopher E. Overton, Lauren H. K. Chappell, Katrina A. Lythgoe, Elizabeth Fearon, Emma Bennett, Jacob Curran-Sebastian, Rajenki Das, Martyn Fyles, Hugo Lewkowicz, Xiaoxi Pang, Bindu Vekaria, Luke Webb, Thomas House, Ian Hall

Early assessments of the spreading rate of COVID-19 were subject to significant uncertainty, as expected with limited data and difficulties in case ascertainment, but more reliable inferences can now be made.

Populations and Evolution