Dengue modeling in rural Cambodia: Statistical performance versus epidemiological relevance
Publication date: Available online 29 August 2018Source: EpidemicsAuthor(s): Clara Champagne, Richard Paul, Sowath Ly, Veasna Duong, Rithea Leang, Bernard CazellesAbstractDengue dynamics are shaped by the complex interplay between several factors, including vector seasonality, interaction between four virus serotypes, and inapparent infections. However, paucity or quality of data do not allow for all of these to be taken into account in mathematical models. In order to explore separately the importance of these factors in models, we combined surveillance data with a local-scale cluster study in the rural province of Kampon...
Source: Epidemics - August 31, 2018 Category: Epidemiology Source Type: research
Patterns of seasonal influenza activity in U.S. core based statistical areas, described using prescriptions of oseltamivir in Medicare claims data
Publication date: Available online 29 August 2018Source: EpidemicsAuthor(s): F. Scott Dahlgren, David K. Shay, Hector S. Izurieta, Richard A. Forshee, Michael Wernecke, Yoganand Chillarige, Yun Lu, Jeffrey A. Kelman, Carrie ReedAbstractUsing Medicare claims data on prescriptions of oseltamivir dispensed to people 65 years old and older, we present a descriptive analysis of patterns of influenza activity in the United States for 579 core based statistical areas (CBSAs) from the 2010–2011 through the 2015–2016 influenza seasons. During this time, 1,010,819 beneficiaries received a prescription of oseltamivir, ranging fro...
Source: Epidemics - August 29, 2018 Category: Epidemiology Source Type: research
A partly stage-structured model for the abundance of salmon lice in salmonid farms
Publication date: Available online 18 August 2018Source: EpidemicsAuthor(s): Aldrin M., Jansen P.A., Stryhn H.AbstractThe parasitic salmon louse constrains growth in the Norwegian salmon farming industry through density dependent host-parasite interaction. Hence, there is a need for insight into how increases in salmon production, varying spatial organisation of the production and pest control strategies affect salmon louse population dynamics. Here we present a new salmon louse model for exploring effects of varying salmon farming conditions on spatio-temporal abundances of the parasite. The salmon louse model is partly s...
Source: Epidemics - August 18, 2018 Category: Epidemiology Source Type: research
Modeling epidemics: A primer and Numerus Model Builder implementation
Publication date: Available online 12 July 2018Source: EpidemicsAuthor(s): Wayne M. Getz, Richard Salter, Oliver Muellerklein, Hyun S. Yoon, Krti TallamAbstractEpidemiological models are dominated by compartmental models, of which SIR formulations are the most commonly used. These formulations can be continuous or discrete (in either the state-variable values or time), deterministic or stochastic, or spatially homogeneous or heterogeneous, the latter often embracing a network formulation. Here we review the continuous and discrete deterministic and discrete stochastic formulations of the SIR dynamical systems models, and w...
Source: Epidemics - July 13, 2018 Category: Epidemiology Source Type: research
Acute illness from Campylobacter jejuni may require high doses while infection occurs at low doses
Publication date: Available online 8 February 2018Source: EpidemicsAuthor(s): Peter F.M. Teunis, Axel Bonačić Marinović, David R. Tribble, Chad K. Porter, Arno SwartAbstractData from a set of different studies on the infectivity and pathogenicity of Campylobacter jejuni were analyzed with a multilevel model, allowing for effects of host species (nonhuman primates and humans) and different strains of the pathogen.All challenge studies involved high doses of the pathogen, resulting in all exposed subjects to become infected. In only one study a dose response effect (increasing trend with dose) for infection was observed. ...
Source: Epidemics - July 11, 2018 Category: Epidemiology Source Type: research
The distribution of district-level leprosy incidence in India is geometric-stable, consistent with subcriticality
Publication date: Available online 14 February 2018Source: EpidemicsAuthor(s): Thomas M. Lietman, Lee Worden, Fengchen Liu, Travis C. PorcoAbstractMathematical models predict that the community-level incidence of a controlled infectious disease across a region approaches a geometric distribution. This could hold over larger regions, if new cases remain proportional to existing cases. Leprosy has been disappearing for centuries, making an excellent candidate for testing this hypothesis. Here, we show the annual new case detection rate of leprosy in Indian districts to be consistent with a geometric distribution. For 2008–...
Source: Epidemics - July 11, 2018 Category: Epidemiology Source Type: research
Results from the second year of a collaborative effort to forecast influenza seasons in the United States
Publication date: Available online 24 February 2018Source: EpidemicsAuthor(s): Matthew Biggerstaff, Michael Johansson, David Alper, Logan C. Brooks, Prithwish Chakraborty, David C. Farrow, Sangwon Hyun, Sasikiran Kandula, Craig McGowan, Naren Ramakrishnan, Roni Rosenfeld, Jeffrey Shaman, Rob Tibshirani, Ryan J. Tibshirani, Alessandro Vespignani, Wan Yang, Qian Zhang, Carrie ReedAbstractAccurate forecasts could enable more informed public health decisions. Since 2013, CDC has worked with external researchers to improve influenza forecasts by coordinating seasonal challenges for the United States and the 10 Health and Human ...
Source: Epidemics - July 11, 2018 Category: Epidemiology Source Type: research
Identifying genotype specific elevated-risk areas and associated herd risk factors for bovine tuberculosis spread in British cattle
Publication date: Available online 1 March 2018Source: EpidemicsAuthor(s): R.J. Orton, M. Deason, P.R. Bessell, D.M. Green, R.R. Kao, L.C.M. SalvadorAbstractBovine tuberculosis (bTB) is a chronic zoonosis with major health and economic impact on the cattle industry. Despite extensive control measures in cattle and culling trials in wildlife, the reasons behind the expansion of areas with high incidence of bTB breakdowns in Great Britain remain unexplained. By balancing the importance of cattle movements and local transmission on the observed pattern of cattle outbreaks, we identify areas at elevated risk of infection from ...
Source: Epidemics - July 11, 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 11, 2018 Category: Epidemiology Source Type: research
Two approaches to forecast Ebola synthetic epidemics
We describe fitting and forecasting procedures for each model and discuss their advantages and drawbacks. We did not find that one model was consistently better in forecasting than the other. (Source: Epidemics)
Source: Epidemics - July 11, 2018 Category: Epidemiology Source Type: research
Using data-driven agent-based models for forecasting emerging infectious diseases
We describe the various components of the model, the calibration process and summarize the forecast performance across scenarios of the challenge. We conclude by highlighting how such a data-driven approach can be refined and adapted for future epidemics, and share the lessons learned over the course of the challenge. (Source: Epidemics)
Source: Epidemics - July 11, 2018 Category: Epidemiology Source Type: research
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 11, 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 11, 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 11, 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 11, 2018 Category: Epidemiology Source Type: research
