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Henrik Salje, Derek A T Cummings, Justin Lessler
The average spatial distance between transmission-linked cases is a fundamental property of infectious disease dispersal. However, the distance between a case and their infector is rarely measurable. Contact-tracing investigations are resource intensive or even impossible, particularly when only a subset of cases are detected. Here, we developed an approach that uses onset dates, the generation time distribution and location information to estimate the mean transmission distance. We tested our method using outbreak simulations...
October 7, 2016: Epidemics
Ashleigh R Tuite, David N Fisman
Mathematical 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" model), which relies only on case counts, in the REFC...
September 28, 2016: Epidemics
Xiong Xiao, Albert Jan van Hoek, Michael G Kenward, Alessia Melegaro, Mark Jit
OBJECTIVE: Infectious disease spread depends on contact rates between infectious and susceptible individuals. Transmission models are commonly informed using empirically collected contact data, but the relevance of different contact types to transmission is still not well understood. Some studies select contacts based on a single characteristic such as proximity (physical/non-physical), location, duration or frequency. This study aimed to explore whether clusters of contacts similar to each other across multiple characteristics could better explain disease transmission...
August 26, 2016: Epidemics
José Lourenço, Mario Recker
Dengue is one of the most important and wide-spread viral infections affecting human populations. The last few decades have seen a dramatic increase in the global burden of dengue, with the virus now being endemic or near-endemic in over 100 countries world-wide. A recombinant tetravalent vaccine candidate (CYD-TDV) has recently completed Phase III clinical efficacy trials in South East Asia and Latin America and has been licensed for use in several countries. The trial results showed moderate-to-high efficacies in protection against clinical symptoms and hospitalisation but with so far unknown effects on transmission and infections per se...
September 2016: Epidemics
P F M Teunis, J C H van Eijkeren, W F de Graaf, A Bonačić Marinović, M E E Kretzschmar
A recently published model for the serum antibody response to infection appeared well suited for use in statistical analyses of longitudinal serological data. The published model assumed exponential decay with fixed rates for pathogen and serum antibody kinetics, ignoring any within-host heterogeneity in the seroresponse. A bi-exponential model shows that there is rapid initial decay followed by a prolonged period of persistent low serum antibody concentrations. We propose a small modification of the decay model that greatly increases its flexibility by allowing for non-exponential antibody decay...
September 2016: Epidemics
Damon J A Toth, Windy D Tanner, Karim Khader, Adi V Gundlapalli
We quantify outbreak risk after importations of Middle East respiratory syndrome outside the Arabian Peninsula. Data from 31 importation events show strong statistical support for lower transmissibility after early transmission generations. Our model projects the risk of ≥10, 100, and 500 transmissions as 11%, 2%, and 0.02%, and ≥1, 2, 3, and 4 generations as 23%, 14%, 0.9%, and 0.05%, respectively. Our results suggest tempered risk of large, long-lasting outbreaks with appropriate control measures.
September 2016: Epidemics
T M Kinyanjui, L Pellis, T House
Household structure is a key driver of many infectious diseases, as well as a natural target for interventions such as vaccination programs. Many theoretical and conceptual advances on household-stratified epidemic models are relatively recent, but have successfully managed to increase the applicability of such models to practical problems. To be of maximum realism and hence benefit, they require parameterisation from epidemiological data, and while household-stratified final size data has been the traditional source, increasingly time-series infection data from households are becoming available...
September 2016: Epidemics
Matthew A Rittenhouse, Crawford W Revie, Amy Hurford
Sea lice (Lepeophtheirus salmonis) are a significant source of monetary losses on salmon farms. Sea lice exhibit temperature-dependent development rates and salinity-dependent mortality, but to date no deterministic models have incorporated these seasonally varying factors. To understand how environmental variation and life history characteristics affect sea lice abundance, we derive a delay differential equation model and parameterize the model with environmental data from British Columbia and southern Newfoundland...
September 2016: Epidemics
J C Blackwood, D A T Cummings, S Iamsirithaworn, P Rohani
Pertussis is a highly infectious respiratory disease that has been on the rise in many countries worldwide over the past several years. The drivers of this increase in pertussis incidence remain hotly debated, with a central and long-standing hypothesis that questions the ability of vaccines to eliminate pertussis transmission rather than simply modulate the severity of disease. In this paper, we present age-structured case notification data from all provinces of Thailand between 1981 and 2014, a period during which vaccine uptake rose substantially, permitting an evaluation of the transmission impacts of vaccination...
September 2016: Epidemics
Jessica Enright, Rowland R Kao
Calculation of expected outbreak size of a simple contagion on a known contact network is a common and important epidemiological task, and is typically carried out by computationally intensive simulation. We describe an efficient exact method to calculate the expected outbreak size of a contagion on an outbreak-invariant network that is a directed and acyclic, allowing us to model all dynamically changing networks when contagion can only travel forward in time. We describe our algorithm and its use in pseudocode, as well as showing examples of its use on disease relevant, data-derived networks...
September 2016: Epidemics
Alexandra B Hogan, Robert S Anderssen, Stephanie Davis, Hannah C Moore, Faye J Lim, Parveen Fathima, Kathryn Glass
Respiratory syncytial virus (RSV) causes respiratory illness in young children and is most commonly associated with bronchiolitis. RSV typically occurs as annual or biennial winter epidemics in temperate regions, with less pronounced seasonality in the tropics. We sought to characterise and compare the seasonality of RSV and bronchiolitis in temperate and tropical Western Australia. We examined over 13 years of RSV laboratory identifications and bronchiolitis hospitalisations in children, using an extensive linked dataset from Western Australia...
September 2016: Epidemics
Hiroshi Nishiura, Kenji Mizumoto, Kat S Rock, Yohei Yasuda, Ryo Kinoshita, Yuichiro Miyamatsu
OBJECTIVES: There has been a growing concern over Zika virus (ZIKV) infection, particularly since a probable link between ZIKV infection during pregnancy and microcephaly in the baby was identified. The present study aimed to estimate a theoretical risk of microcephaly during pregnancy with ZIKV infection in Northeastern Brazil in 2015. METHODS: Temporal distributions of microcephaly, reported dengue-like illness and dengue seropositive in Brazil were extracted from secondary data sources...
June 2016: Epidemics
Chris R Kenyon, Achilleas Tsoumanis, Ilan Steven Schwartz
BACKGROUND: Given the large variation in the prevalence of sexually transmitted infections between populations it is important to characterize how sexual vary between populations. In this paper we assess how the distribution of lifetime sexual partners varies between populations. We ask: do populations with higher mean lifetime sexual partners merely differ by virtue of the presence of a core-group with increased number of partners or do the population distributions move as more coherent wholes? METHODS: We defined those in the top decile of lifetime sex partners in each country as constituting the higher-risk behaviour group (HRB)...
June 2016: Epidemics
Allison E Aiello, Amanda M Simanek, Marisa C Eisenberg, Alison R Walsh, Brian Davis, Erik Volz, Caroline Cheng, Jeanette J Rainey, Amra Uzicanin, Hongjiang Gao, Nathaniel Osgood, Dylan Knowles, Kevin Stanley, Kara Tarter, Arnold S Monto
BACKGROUND: Social networks are increasingly recognized as important points of intervention, yet relatively few intervention studies of respiratory infection transmission have utilized a network design. Here we describe the design, methods, and social network structure of a randomized intervention for isolating respiratory infection cases in a university setting over a 10-week period. METHODOLOGY/PRINCIPAL FINDINGS: 590 students in six residence halls enrolled in the eX-FLU study during a chain-referral recruitment process from September 2012-January 2013...
June 2016: Epidemics
Cécile Viboud, Lone Simonsen, Gerardo Chowell
BACKGROUND: A better characterization of the early growth dynamics of an epidemic is needed to dissect the important drivers of disease transmission, refine existing transmission models, and improve disease forecasts. MATERIALS AND METHODS: We introduce a 2-parameter generalized-growth model to characterize the ascending phase of an outbreak and capture epidemic profiles ranging from sub-exponential to exponential growth. We test the model against empirical outbreak data representing a variety of viral pathogens in historic and contemporary populations, and provide simulations highlighting the importance of sub-exponential growth for forecasting purposes...
June 2016: Epidemics
Thomas J R Finnie, Andy South, Ana Bento, Ellie Sherrard-Smith, Thibaut Jombart
Epidemiology relies on data but the divergent ways data are recorded and transferred, both within and between outbreaks, and the expanding range of data-types are creating an increasingly complex problem for the discipline. There is a need for a consistent, interpretable and precise way to transfer data while maintaining its fidelity. We introduce 'EpiJSON', a new, flexible, and standards-compliant format for the interchange of epidemiological data using JavaScript Object Notation. This format is designed to enable the widest range of epidemiological data to be unambiguously held and transferred between people, software and institutions...
June 2016: Epidemics
William J M Probert, Katriona Shea, Christopher J Fonnesbeck, Michael C Runge, Tim E Carpenter, Salome Dürr, M Graeme Garner, Neil Harvey, Mark A Stevenson, Colleen T Webb, Marleen Werkman, Michael J Tildesley, Matthew J Ferrari
Formal decision-analytic methods can be used to frame disease control problems, the first step of which is to define a clear and specific objective. We demonstrate the imperative of framing clearly-defined management objectives in finding optimal control actions for control of disease outbreaks. We illustrate an analysis that can be applied rapidly at the start of an outbreak when there are multiple stakeholders involved with potentially multiple objectives, and when there are also multiple disease models upon which to compare control actions...
June 2016: Epidemics
Chiara Poletto, Vittoria Colizza, Pierre-Yves Boëlle
MERS coronavirus cases notified in the Middle East region since the identification of the virus in 2012 have displayed variations in time and across geography. Through a combined modelling approach, we estimate the rates of generation of cases along the zoonotic and human-to-human transmission routes and assess their spatiotemporal heterogeneity. We consider all cases notified to WHO from March 2012 to mid-September 2014. We use a stochastic modelling of the time series of case incidence in the Middle East region to estimate time- and space-dependent zoonotic and human-to-human transmission parameters...
June 2016: Epidemics
Erida Gjini, M Gabriela M Gomes
The efficacy of vaccines is typically estimated prior to implementation, on the basis of randomized controlled trials. This does not preclude, however, subsequent assessment post-licensure, while mass-immunization and nonlinear transmission feedbacks are in place. In this paper we show how cross-sectional prevalence data post-vaccination can be interpreted in terms of pathogen transmission processes and vaccine parameters, using a dynamic epidemiological model. We advocate the use of such frameworks for model-based vaccine evaluation in the field, fitting trajectories of cross-sectional prevalence of pathogen strains before and after intervention...
March 2016: Epidemics
Zindoga Mukandavire, Kate M Mitchell, Peter Vickerman
In many settings, interventions targeting female sex workers (FSWs) could significantly reduce the overall transmission of HIV. To understand the role HIV pre-exposure prophylaxis (PrEP) could play in controlling HIV transmission amongst FSWs, it is important to understand how its impact compares with scaling-up condom use-one of the proven HIV prevention strategies for FSWs. It is important to remember that condoms also have other benefits such as reducing the incidence of sexually transmitted infections and preventing pregnancy...
March 2016: Epidemics
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