Approximate Bayesian Computation for infectious disease modelling
We present a tutorial on coding practice for ABC in R and three case studies to illustrate the application of ABC to infectious disease models. (Source: Epidemics)
Source: Epidemics - September 26, 2019 Category: Epidemiology Source Type: research
Ensemble Forecast and Parameter Inference of Childhood Diarrhea in Chobe District, Botswana
Publication date: Available online 16 September 2019Source: EpidemicsAuthor(s): Alexandra Heaney, Kathleen A. Alexander, Jeffrey ShamanAbstractDiarrheal disease is the second largest cause of mortality in children younger than 5, yet our ability to anticipate and prepare for outbreaks remains limited. Here, we develop and test an epidemiological forecast model for childhood diarrheal disease in Chobe District, Botswana. Our prediction system uses a compartmental susceptible-infected-recovered-susceptible (SIRS) model coupled with Bayesian data assimilation to infer relevant epidemiological parameter values and generate ret...
Source: Epidemics - September 17, 2019 Category: Epidemiology Source Type: research
Accurate forecasts of the effectiveness of interventions against Ebola may require models that account for variations in symptoms during infection
Publication date: Available online 11 September 2019Source: EpidemicsAuthor(s): W.S. Hart, L.F.R. Hochfilzer, N.J. Cunniffe, H. Lee, H. Nishiura, R.N. ThompsonAbstractEpidemiological models are routinely used to predict the effects of interventions aimed at reducing the impacts of Ebola epidemics. Most models of interventions targeting symptomatic hosts, such as isolation or treatment, assume that all symptomatic hosts are equally likely to be detected. In other words, following an incubation period, the level of symptoms displayed by an individual host is assumed to remain constant throughout an infection. In reality, how...
Source: Epidemics - September 12, 2019 Category: Epidemiology Source Type: research
Tackling hepatitis E virus spread and persistence on farrow-to-finish pig farms: insights from a stochastic individual-based multi-pathogen model
The objective of this study was to develop a multi-pathogen modelling approach to understand the conditions under which HEV spreads and persists on a farrow-to-finish pig farm taking into account the fact that pigs may be co-infected with an intercurrent pathogen. A stochastic individual-based model was therefore designed that combines a population dynamics model, which enables us to take different batch rearing systems into account, with a multi-pathogen model representing at the same time the dynamics of both HEV and the intercurrent pathogen. Based on experimental and field data, the epidemiological parameters of the HE...
Source: Epidemics - September 1, 2019 Category: Epidemiology Source Type: research
Publisher's Note
Publication date: Available online 28 August 2019Source: EpidemicsAuthor(s): (Source: Epidemics)
Source: Epidemics - August 29, 2019 Category: Epidemiology Source Type: research
Improved inference of time-varying reproduction numbers during infectious disease outbreaks
We present a tool for estimating the reproduction number in real-time during infectious disease outbreaks accurately, which is available as an R software package (EpiEstim 2.2). It is also accessible as an interactive, user-friendly online interface (EpiEstim App), permitting its use by non-specialists. Our tool is easy to apply for assessing the transmission potential, and hence informing control, during future outbreaks of a wide range of invading pathogens. (Source: Epidemics)
Source: Epidemics - August 27, 2019 Category: Epidemiology Source Type: research
Spatial Analysis Made Easy with Linear Regression and Kernels
Publication date: Available online 21 August 2019Source: EpidemicsAuthor(s): Philip Milton, Helen Coupland, Emanuele Giorgi, Samir BhattAbstractKernel methods are a popular technique for extending linear models to handle non-linear spatial problems via a mapping to an implicit, high-dimensional feature space. While kernel methods are computationally cheaper than an explicit feature mapping, they are still subject to cubic cost on the number of points. Given only a few thousand locations, this computational cost rapidly outstrips the currently available computational power. This paper aims to provide an overview of kernel m...
Source: Epidemics - August 22, 2019 Category: Epidemiology Source Type: research
Predicting the impact of clustered risk and testing behaviour patterns on the population-level effectiveness of pre-exposure prophylaxis against HIV among gay, bisexual and other men who have sex with men in Greater Vancouver, Canada
Publication date: Available online 19 August 2019Source: EpidemicsAuthor(s): Michael A. Irvine, Travis Salway, Troy Grennan, Jason Wong, Mark Gilbert, Daniel CoombsAbstractPre-exposure prophylaxis (PrEP) has the potential to greatly reduce transmission of HIV. However, significant questions remain around how behavioural factors may influence its impact within target populations. We used a 2014 sexual behaviour survey to modify and recalibrate a mathematical model of HIV infection dynamics within the population of gay, bisexual and other men who have sex with men (GBMSM) in the Greater Vancouver area of British Columbia, Ca...
Source: Epidemics - August 20, 2019 Category: Epidemiology Source Type: research
Real-time predictions of the 2018–2019 Ebola virus disease outbreak in the Democratic Republic of the Congo using Hawkes point process models
Publication date: Available online 23 July 2019Source: EpidemicsAuthor(s): J. Daniel Kelly, Junhyung Park, Ryan J. Harrigan, Nicole A. Hoff, Sarita D. Lee, Rae Wannier, Bernice Selo, Mathias Mossoko, Bathe Njoloko, Emile Okitolonda-Wemakoy, Placide Mbala-Kingebeni, George W. Rutherford, Thomas B. Smith, Steve Ahuka-Mundeke, Jean Jacques Muyembe-Tamfum, Anne W. Rimoin, Frederic Paik SchoenbergAbstractAs of June 16, 2019, an Ebola virus disease (EVD) outbreak has led to 2136 reported cases in the northeastern region of the Democratic Republic of the Congo (DRC). As this outbreak continues to threaten the lives and livelihood...
Source: Epidemics - August 7, 2019 Category: Epidemiology Source Type: research
A framework for evaluating the effects of observational type and quality on vector-borne disease forecast
Publication date: Available online 5 August 2019Source: EpidemicsAuthor(s): Teresa K. Yamana, Jeffrey ShamanAbstractRecent research has advanced infectious disease forecasting from an aspiration to an operational reality. The accuracy of such operational forecasting depends on the quantity and quality of observations available for system optimization. In particular, for forecasting systems that use combined mechanistic model-inference approaches, a broad suite of epidemiological observations could be utilized, if these data were available in near real time. In cases where such data are limited, an in silica, synthetic fram...
Source: Epidemics - August 5, 2019 Category: Epidemiology Source Type: research
Estimating the impact of violent events on transmission in Ebola virus disease outbreak, Democratic Republic of the Congo, 2018–2019
ConclusionThe difference in the estimated transmission rates between zones affected by recent violent events suggests that violent events are contributing to increased transmission and the ongoing nature of this outbreak. (Source: Epidemics)
Source: Epidemics - July 27, 2019 Category: Epidemiology Source Type: research
Real-time predictions of the 2018-2019 Ebola virus disease outbreak in the Democratic Republic of the Congo using Hawkes point process models
Publication date: Available online 23 July 2019Source: EpidemicsAuthor(s): J. Daniel Kelly, Junhyung Park, Ryan J. Harrigan, Nicole A. Hoff, Sarita D. Lee, Rae Wannier, Bernice Selo, Mathias Mossoko, Bathe Njoloko, Emile Okitolonda-Wemakoy, Placide Mbala-Kingebeni, George W. Rutherford, Thomas B. Smith, Steve Ahuka-Mundeke, Jean Jacques Muyembe-Tamfum, Anne W. Rimoin, Frederic Paik SchoenbergAbstractAs of June 16, 2019, an Ebola virus disease (EVD) outbreak has led to 2136 reported cases in the northeastern region of the Democratic Republic of the Congo (DRC). As this outbreak continues to threaten the lives and livelihood...
Source: Epidemics - July 25, 2019 Category: Epidemiology Source Type: research
Analyzing Influenza Outbreaks in Russia Using an Age-structured Dynamic Transmission Model
In this study, we addressed the ability of a minimalistic SEIR model to satisfactorily describe influenza outbreak dynamics in Russian settings. For that purpose, we calibrated an age-specific influenza dynamics model to Russian acute respiratory infection (ARI) incidence data over 2009-2016 and assessed the variability of proportion of non-immune individuals in the population depending on the regarded city, the non-epidemic indicence baseline, the contact structure considered and the used calibration method. The experiments demonstrated the importance of distinguishing characteristics of different age groups, such as cont...
Source: Epidemics - July 23, 2019 Category: Epidemiology Source Type: research
Heterogeneous local dynamics revealed by classification analysis of spatially disaggregated time series data
Publication date: Available online 22 July 2019Source: EpidemicsAuthor(s): T. Alex Perkins, Isabel Rodriguez-Barraquer, Carrie Manore, Amir S. Siraj, Guido España, Christopher M. Barker, Michael A. Johansson, Robert C. ReinerAbstractTime series data provide a crucial window into infectious disease dynamics, yet their utility is often limited by the spatially aggregated form in which they are presented. When working with time series data, violating the implicit assumption of homogeneous dynamics below the scale of spatial aggregation could bias inferences about underlying processes. We tested this assumption in the context...
Source: Epidemics - July 23, 2019 Category: Epidemiology Source Type: research
The drivers of squirrelpox virus dynamics in its grey squirrel reservoir host
Publication date: Available online 15 July 2019Source: EpidemicsAuthor(s): Julian Chantrey, Timothy Dale, David Jones, Michael Begon, Andy FentonAbstractMany pathogens of conservation concern circulate endemically within natural wildlife reservoir hosts and it is imperative to understand the individual and ecological drivers of natural transmission dynamics, if any threat to a related endangered species is to be assessed. Our study highlights the key drivers of infection and shedding dynamics of squirrelpox virus (SQPV) in its reservoir grey squirrel (Sciurus carolinensis) population. To clarify SQPV dynamics in this popul...
Source: Epidemics - July 16, 2019 Category: Epidemiology Source Type: research
