title: A simple approach to measure transmissibility and forecast incidence.
abstract: Outbreaks of novel pathogens such as SARS, pandemic influenza and Ebola require substantial investments in reactive interventions, with consequent implementation plans sometimes revised on a weekly basis. Therefore, short-term forecasts of incidence are often of high priority. In light of the recent Ebola epidemic in West Africa, a forecasting exercise was convened by a network of infectious disease modellers. The challenge was to forecast unseen "future" simulated data for four different scenarios at five different time points. In a similar method to that used during the recent Ebola epidemic, we estimated current levels of transmissibility, over variable time-windows chosen in an ad hoc way. Current estimated transmissibility was then used to forecast near-future incidence. We performed well within the challenge and often produced accurate forecasts. A retrospective analysis showed that our subjective method for deciding on the window of time with which to estimate transmissibility often resulted in the optimal choice. However, when near-future trends deviated substantially from exponential patterns, the accuracy of our forecasts was reduced. This exercise highlights the urgent need for infectious disease modellers to develop more robust descriptions of processes - other than the widespread depletion of susceptible individuals - that produce non-exponential patterns of incidence.
authors.affiliation: MRC Centre for Outbreak Analysis and Modelling, Imperial College London, Faculty of Medicine, London, UK; National Institute for Health Research Health Protection Research Unit in Modelling Methodology, Imperial College London, Faculty of Medicine, London, UK.
authors.forename: Pierre
authors.initials: P
authors.lastname: Nouvellet
authors.affiliation: MRC Centre for Outbreak Analysis and Modelling, Imperial College London, Faculty of Medicine, London, UK.
authors.forename: Anne
authors.initials: A
authors.lastname: Cori
authors.affiliation: MRC Centre for Outbreak Analysis and Modelling, Imperial College London, Faculty of Medicine, London, UK.
authors.forename: Tini
authors.initials: T
authors.lastname: Garske
authors.affiliation: MRC Centre for Outbreak Analysis and Modelling, Imperial College London, Faculty of Medicine, London, UK.
authors.forename: Isobel M
authors.initials: IM
authors.lastname: Blake
authors.affiliation: MRC Centre for Outbreak Analysis and Modelling, Imperial College London, Faculty of Medicine, London, UK.
authors.forename: Ilaria
authors.initials: I
authors.lastname: Dorigatti
authors.affiliation: MRC Centre for Outbreak Analysis and Modelling, Imperial College London, Faculty of Medicine, London, UK.
authors.forename: Wes
authors.initials: W
authors.lastname: Hinsley
authors.affiliation: MRC Centre for Outbreak Analysis and Modelling, Imperial College London, Faculty of Medicine, London, UK; National Institute for Health Research Health Protection Research Unit in Modelling Methodology, Imperial College London, Faculty of Medicine, London, UK.
authors.forename: Thibaut
authors.initials: T
authors.lastname: Jombart
authors.affiliation: MRC Centre for Outbreak Analysis and Modelling, Imperial College London, Faculty of Medicine, London, UK.
authors.forename: Harriet L
authors.initials: HL
authors.lastname: Mills
authors.affiliation: MRC Centre for Outbreak Analysis and Modelling, Imperial College London, Faculty of Medicine, London, UK.
authors.forename: Gemma
authors.initials: G
authors.lastname: Nedjati-Gilani
authors.affiliation: MRC Centre for Outbreak Analysis and Modelling, Imperial College London, Faculty of Medicine, London, UK; Center for Global Health, Institute Pasteur, Paris, France.
authors.forename: Maria D
authors.initials: MD
authors.lastname: Van Kerkhove
authors.affiliation: MRC Centre for Outbreak Analysis and Modelling, Imperial College London, Faculty of Medicine, London, UK; National Institute for Health Research Health Protection Research Unit in Modelling Methodology, Imperial College London, Faculty of Medicine, London, UK.
authors.forename: Christophe
authors.initials: C
authors.lastname: Fraser
authors.affiliation: MRC Centre for Outbreak Analysis and Modelling, Imperial College London, Faculty of Medicine, London, UK; National Institute for Health Research Health Protection Research Unit in Modelling Methodology, Imperial College London, Faculty of Medicine, London, UK.
authors.forename: Christl A
authors.initials: CA
authors.lastname: Donnelly
authors.affiliation: MRC Centre for Outbreak Analysis and Modelling, Imperial College London, Faculty of Medicine, London, UK; National Institute for Health Research Health Protection Research Unit in Modelling Methodology, Imperial College London, Faculty of Medicine, London, UK.
authors.forename: Neil M
authors.initials: NM
authors.lastname: Ferguson
authors.affiliation: MRC Centre for Outbreak Analysis and Modelling, Imperial College London, Faculty of Medicine, London, UK; National Institute for Health Research Health Protection Research Unit in Modelling Methodology, Imperial College London, Faculty of Medicine, London, UK. Electronic address: s.riley@imperial.ac.uk.
authors.forename: Steven
authors.initials: S
authors.lastname: Riley
mesh_terms: D003141:Communicable Diseases / Q000453:epidemiology* / Q000635:transmission*; D058872:Epidemics / Q000706:statistics & numerical data*; D005544:Forecasting; D006801:Humans; D015994:Incidence; D012189:Retrospective Studies
keywords: Branching process; Forecasting; MCMC; Rapid response; Renewal equation