Forecasting Ebola with a regression transmission model
We describe a relatively simple stochastic model of Ebola transmission that was used to produce forecasts with the lowest mean absolute error among Ebola Forecasting Challenge participants. The model enabled prediction of peak incidence, the timing of this peak, and final size of the outbreak. The underlying discrete-time compartmental model used a time-varying reproductive rate modeled as a multiplicative random walk driven by the number of infectious individuals. This structure generalizes traditional Susceptible-Infected-Recovered (SIR) disease modeling approaches and allows for the flexible consideration of outbreaks w...
Source: Epidemics - July 5, 2018 Category: Epidemiology Source Type: research
Real-time forecasting of infectious disease dynamics with a stochastic semi-mechanistic model
Publication date: March 2018Source: Epidemics, Volume 22Author(s): Sebastian Funk, Anton Camacho, Adam J. Kucharski, Rosalind M. Eggo, W. John EdmundsAbstractReal-time forecasts of infectious diseases can help public health planning, especially during outbreaks. If forecasts are generated from mechanistic models, they can be further used to target resources or to compare the impact of possible interventions. However, paremeterising such models is often difficult in real time, when information on behavioural changes, interventions and routes of transmission are not readily available. Here, we present a semi-mechanistic mode...
Source: Epidemics - July 5, 2018 Category: Epidemiology Source Type: research
Using phenomenological models for forecasting the 2015 Ebola challenge
ConclusionsOur findings further support the consideration of transmission models that incorporate flexible early epidemic growth profiles in the forecasting toolkit. Such models are particularly useful for quickly evaluating a developing infectious disease outbreak using only case incidence time series of the early phase of an infectious disease outbreak. (Source: Epidemics)
Source: Epidemics - July 5, 2018 Category: Epidemiology Source Type: research
The IDEA model: A single equation approach to the Ebola forecasting challenge
Publication date: March 2018Source: Epidemics, Volume 22Author(s): Ashleigh R. Tuite, David N. FismanAbstractMathematical modeling is increasingly accepted as a tool that can inform disease control policy in the face of emerging infectious diseases, such as the 2014–2015 West African Ebola epidemic, but little is known about the relative performance of alternate forecasting approaches. The RAPIDD Ebola Forecasting Challenge (REFC) tested the ability of eight mathematical models to generate useful forecasts in the face of simulated Ebola outbreaks. We used a simple, phenomenological single-equation model (the “IDEA” m...
Source: Epidemics - July 5, 2018 Category: Epidemiology Source Type: research
IFC, Ed Board
Publication date: March 2018Source: Epidemics, Volume 22Author(s): (Source: Epidemics)
Source: Epidemics - July 5, 2018 Category: Epidemiology Source Type: research
The RAPIDD Ebola forecasting challenge special issue: Preface
Publication date: March 2018Source: Epidemics, Volume 22Author(s): Cécile Viboud, Lone Simonsen, Gerardo Chowell, Alessandro Vespignani (Source: Epidemics)
Source: Epidemics - July 5, 2018 Category: Epidemiology Source Type: research
The RAPIDD Ebola forecasting challenge: Model description and synthetic data generation
Publication date: March 2018Source: Epidemics, Volume 22Author(s): Marco Ajelli, Qian Zhang, Kaiyuan Sun, Stefano Merler, Laura Fumanelli, Gerardo Chowell, Lone Simonsen, Cecile Viboud, Alessandro VespignaniAbstractThe Ebola forecasting challenge organized by the Research and Policy for Infectious Disease Dynamics (RAPIDD) program of the Fogarty International Center relies on synthetic disease datasets generated by numerical simulations of a highly detailed spatially-structured agent-based model. We discuss here the architecture and technical steps of the challenge, leading to datasets that mimic as much as possible the da...
Source: Epidemics - July 5, 2018 Category: Epidemiology Source Type: research
The RAPIDD ebola forecasting challenge: Synthesis and lessons learnt
Publication date: March 2018Source: Epidemics, Volume 22Author(s): Cécile Viboud, Kaiyuan Sun, Robert Gaffey, Marco Ajelli, Laura Fumanelli, Stefano Merler, Qian Zhang, Gerardo Chowell, Lone Simonsen, Alessandro Vespignani, the RAPIDD Ebola Forecasting Challenge groupAbstractInfectious disease forecasting is gaining traction in the public health community; however, limited systematic comparisons of model performance exist. Here we present the results of a synthetic forecasting challenge inspired by the West African Ebola crisis in 2014–2015 and involving 16 international academic teams and US government agencies, and co...
Source: Epidemics - July 5, 2018 Category: Epidemiology Source Type: research
Application of the CDC EbolaResponse Modeling tool to disease predictions
Publication date: March 2018Source: Epidemics, Volume 22Author(s): Robert H. Gaffey, Cécile ViboudAbstractModel-based predictions were critical in eliciting a vigorous international public health response to the 2014 Ebola Virus Disease outbreak in West Africa. Here, we describe the performances of an extension of the CDC-initiated EbolaResponse Modeling tool to the Ebola Forecasting Challenge, which offered a controlled environment for epidemiological predictions. In the EbolaResponse tool, transmission risks and proportions of population affected by interventions were fitted to data via least square fitting. Prediction ...
Source: Epidemics - July 5, 2018 Category: Epidemiology Source Type: research
A simple approach to measure transmissibility and forecast incidence
Publication date: March 2018Source: Epidemics, Volume 22Author(s): Pierre Nouvellet, Anne Cori, Tini Garske, Isobel M. Blake, Ilaria Dorigatti, Wes Hinsley, Thibaut Jombart, Harriet L. Mills, Gemma Nedjati-Gilani, Maria D. Van Kerkhove, Christophe Fraser, Christl A. Donnelly, Neil M. Ferguson, Steven RileyAbstractOutbreaks 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...
Source: Epidemics - July 5, 2018 Category: Epidemiology Source Type: research
Robust qualitative estimation of time-varying contact rates in uncertain epidemics
Publication date: Available online 15 March 2018Source: EpidemicsAuthor(s): Marco Tulio Angulo, Jorge X. Velasco-HernandezAbstractWe will inevitably face new epidemics where the lack of long time-series data and the uncertainty about the outbreak dynamics make difficult to obtain quantitative predictions. Here we present an algorithm to qualitatively infer time-varying contact rates from short time-series data, letting us predict the start, relative magnitude and decline of epidemic outbreaks. Using real time-series data of measles, dengue, and the current zika outbreak, we demonstrate our algorithm can outperform existing...
Source: Epidemics - July 5, 2018 Category: Epidemiology Source Type: research
Transmission dynamics of influenza in two major cities of Uganda
Publication date: Available online 19 March 2018Source: EpidemicsAuthor(s): Wan Yang, Matthew J. Cummings, Barnabas Bakamutumaho, John Kayiwa, Nicholas Owor, Barbara Namagambo, Timothy Byaruhanga, Julius J. Lutwama, Max R. O’Donnell, Jeffrey ShamanAbstractIn this paper, we report the epidemic characteristics of the three co-circulating influenza viruses (i.e., A/H1N1, A/H3N2, and B) in two tropical African cities—Kampala and Entebbe, Uganda—over an eight-year period (2008–2015). Using wavelet methods, we show that influenza epidemics recurred annually during the study period. In most months, two or more influenza v...
Source: Epidemics - July 5, 2018 Category: Epidemiology Source Type: research
Contagion! The BBC Four Pandemic – The model behind the documentary
Publication date: Available online 22 March 2018Source: EpidemicsAuthor(s): Petra Klepac, Stephen Kissler, Julia GogAbstractTo mark the centenary of the 1918 influenza pandemic, the broadcasting network BBC have put together a 75-min documentary called ‘Contagion! The BBC Four Pandemic’. Central to the documentary is a nationwide citizen science experiment, during which volunteers in the United Kingdom could download and use a custom mobile phone app called BBC Pandemic, and contribute their movement and contact data for a day.As the ‘maths team’, we were asked to use the data from the app to build and run a model ...
Source: Epidemics - July 5, 2018 Category: Epidemiology Source Type: research
Age difference between heterosexual partners in Britain: Implications for the spread of Chlamydia trachomatis
This study illustrates how sexual behavior data can be used to reconstruct detailed sexual mixing patterns by age, and how these patterns can be integrated into dynamic transmission models. The proposed framework can be extended to study the effects of age-dependent transmission on incidence in any STI. (Source: Epidemics)
Source: Epidemics - July 5, 2018 Category: Epidemiology Source Type: research
Using state-space models to predict the abundance of juvenile and adult sea lice on Atlantic salmon
In this study, two sets of multivariate autoregressive state-space models were applied to Chilean sea lice data from six Atlantic salmon production cycles on five isolated farms (at least 20 km seaway distance away from other known active farms), to evaluate the utility of these models for predicting sea lice abundance over time on farms. The models were constructed with different parameter configurations, and the analysis demonstrated large heterogeneity between production cycles for the autoregressive parameter, the effects of chemotherapeutant bath treatments, and the process-error variance. A model allowing for diffe...
Source: Epidemics - July 5, 2018 Category: Epidemiology Source Type: research
