Modelling the global spread of diseases: A review of current practice and capability
Publication date: Available online 18 May 2018Source: EpidemicsAuthor(s): Caroline E. Walters, Margaux M.I. Meslé, Ian M. HallAbstractMathematical models can aid in the understanding of the risks associated with the global spread of infectious diseases. To assess the current state of mathematical models for the global spread of infectious diseases, we reviewed the literature highlighting common approaches and good practice, and identifying research gaps. We followed a scoping study method and extracted information from 78 records on: modelling approaches; input data (epidemiological, population, and travel) for model para...
Source: Epidemics - July 11, 2018 Category: Epidemiology Source Type: research
The role of age-mixing patterns in HIV transmission dynamics: Novel hypotheses from a field study in Cape Town, South Africa
Publication date: Available online 18 May 2018Source: EpidemicsAuthor(s): Roxanne Beauclair, Niel Hens, Wim DelvaAbstractBackgroundAge-disparate relationships are thought to put young women at increased risk of HIV, though current evidence is inconclusive. Studying population-level age-mixing patterns as well as individual-level measures of age difference variation may provide insight into the persistence and magnitude of the epidemic in South Africa.MethodsWe used data from a survey in Cape Town (n = 506) to describe age-mixing dynamics in the four population strata of HIV negative and HIV positive male and female par...
Source: Epidemics - July 11, 2018 Category: Epidemiology Source Type: research
Identifying human encounters that shape the transmission of Streptococcus pneumoniae and other acute respiratory infections
Publication date: Available online 19 May 2018Source: EpidemicsAuthor(s): Olivier le Polain de Waroux, Stefan Flasche, Adam J Kucharski, Celine Langendorf, Donny Ndazima, Juliet Mwanga-Amumpaire, Rebecca F Grais, Sandra Cohuet, W John EdmundsAbstractAlthough patterns of social contacts are believed to be an important determinant of infectious disease transmission, it remains unclear how the frequency and nature of human interactions shape an individual’s risk of infection. We analysed data on daily social encounters individually matched to data on S. pneumoniae carriage and acute respiratory symptoms (ARS), from 566 indi...
Source: Epidemics - July 11, 2018 Category: Epidemiology Source Type: research
Tuberculosis outbreak investigation using phylodynamic analysis
In this study, we investigate and compare the epidemiological dynamics underlying two M. tuberculosis outbreaks using phylodynamic methods. Specifically, we (i) test if the outbreak data sets contain enough genetic variation to estimate short-term evolutionary rates and (ii) reconstruct epidemiological parameters such as the effective reproduction number.The first outbreak occurred in the Swiss city of Bern (1987–2012) and was caused by a drug-susceptible strain belonging to the phylogenetic M. tuberculosis Lineage 4. The second outbreak was caused by a multidrug-resistant (MDR) strain of Lineage 2, imported from the Wat...
Source: Epidemics - July 11, 2018 Category: Epidemiology Source Type: research
Kernel-density estimation and approximate Bayesian computation for flexible epidemiological model fitting in Python
Publication date: Available online 26 May 2018Source: EpidemicsAuthor(s): Michael A. Irvine, T. Déirdre HollingsworthAbstractFitting complex models to epidemiological data is a challenging problem: methodologies can be inaccessible to all but specialists, there may be challenges in adequately describing uncertainty in model fitting, the complex models may take a long time to run, and it can be difficult to fully capture the heterogeneity in the data. We develop an adaptive approximate Bayesian computation scheme to fit a variety of epidemiologically relevant data with minimal hyper-parameter tuning by using an adaptive to...
Source: Epidemics - July 11, 2018 Category: Epidemiology Source Type: research
Practical unidentifiability of a simple vector-borne disease model: Implications for parameter estimation and intervention assessment
Publication date: Available online 26 May 2018Source: EpidemicsAuthor(s): Yu-Han Kao, Marisa C. EisenbergAbstractMathematical modeling has an extensive history in vector-borne disease epidemiology, and is increasingly used for prediction, intervention design, and understanding mechanisms. Many studies rely on parameter estimation to link models and data, and to tailor predictions and counterfactuals to specific settings. However, few studies have formally evaluated whether vector-borne disease models can properly estimate the parameters of interest given the constraints of a particular dataset. Identifiability analysis all...
Source: Epidemics - July 11, 2018 Category: Epidemiology Source Type: research
Estimating the effective reproduction number of dengue considering temperature-dependent generation intervals
Publication date: Available online 31 May 2018Source: EpidemicsAuthor(s): Claudia T. Codeço, Daniel A.M. Villela, Flavio C. CoelhoAbstractThe effective reproduction number, Rt, is a measure of transmission that can be calculated from standard incidence data to timely detect the beginning of epidemics. It has being increasingly used for surveillance of directly transmitted diseases. However, current methods for Rt estimation do not apply for vector borne diseases, whose transmission cycle depends on temperature. Here we propose a method that provides dengue's Rt estimates in the presence of temperature-mediated seasonality...
Source: Epidemics - July 11, 2018 Category: Epidemiology Source Type: research
Modeling Marek's disease virus transmission: A framework for evaluating the impact of farming practices and evolution
Publication date: June 2018Source: Epidemics, Volume 23Author(s): David A. Kennedy, Patricia A. Dunn, Andrew F. ReadAbstractMarek's disease virus (MDV) is a pathogen of chickens whose control has twice been undermined by pathogen evolution. Disease ecology is believed to be the main driver of this evolution, yet mathematical models of MDV disease ecology have never been confronted with data to test their reliability. Here, we develop a suite of MDV models that differ in the ecological mechanisms they include. We fit these models with maximum likelihood using iterated filtering in ‘pomp’ to data on MDV concentration in ...
Source: Epidemics - July 11, 2018 Category: Epidemiology Source Type: research
Contact tracing for the control of infectious disease epidemics: Chronic Wasting Disease in deer farms
Publication date: June 2018Source: Epidemics, Volume 23Author(s): Chris Rorres, Maria Romano, Jennifer A. Miller, Jana M. Mossey, Tony H. Grubesic, David E. Zellner, Gary SmithAbstractContact tracing is a crucial component of the control of many infectious diseases, but is an arduous and time consuming process. Procedures that increase the efficiency of contact tracing increase the chance that effective controls can be implemented sooner and thus reduce the magnitude of the epidemic. We illustrate a procedure using Graph Theory in the context of infectious disease epidemics of farmed animals in which the epidemics are driv...
Source: Epidemics - July 11, 2018 Category: Epidemiology Source Type: research
Assessing the variability in transmission of bovine tuberculosis within Spanish cattle herds
Publication date: June 2018Source: Epidemics, Volume 23Author(s): G. Ciaravino, A. García-Saenz, S. Cabras, A. Allepuz, J. Casal, I. García-Bocanegra, A. De Koeijer, S. Gubbins, J.L. Sáez, D. Cano-Terriza, S. NappAbstractIn Spain, despite years of efforts to eradicate bovine tuberculosis (bTB), the disease is still endemic, with some areas of high prevalence. In this context, the surveillance and control plans may need to be re-evaluated, and understanding the dynamics of bTB spread within Spanish herds may help to develop new strategies for reducing the time for detection of infected herds and for the elimination of bT...
Source: Epidemics - July 11, 2018 Category: Epidemiology Source Type: research
A Bayesian evidence synthesis approach to estimate disease prevalence in hard-to-reach populations: hepatitis C in New York City
Publication date: June 2018Source: Epidemics, Volume 23Author(s): Sarah Tan, Susanna Makela, Daliah Heller, Kevin Konty, Sharon Balter, Tian Zheng, James H. StarkAbstractExisting methods to estimate the prevalence of chronic hepatitis C (HCV) in New York City (NYC) are limited in scope and fail to assess hard-to-reach subpopulations with highest risk such as injecting drug users (IDUs). To address these limitations, we employ a Bayesian multi-parameter evidence synthesis model to systematically combine multiple sources of data, account for bias in certain data sources, and provide unbiased HCV prevalence estimates with ass...
Source: Epidemics - July 11, 2018 Category: Epidemiology Source Type: research
IFC, Ed Board
Publication date: June 2018Source: Epidemics, Volume 23Author(s): (Source: Epidemics)
Source: Epidemics - July 11, 2018 Category: Epidemiology Source Type: research
Comparison of cluster-based and source-attribution methods for estimating transmission risk using large HIV sequence databases
Publication date: June 2018Source: Epidemics, Volume 23Author(s): Stéphane Le Vu, Oliver Ratmann, Valerie Delpech, Alison E. Brown, O. Noel Gill, Anna Tostevin, Christophe Fraser, Erik M. VolzAbstractPhylogenetic clustering of HIV sequences from a random sample of patients can reveal epidemiological transmission patterns, but interpretation is hampered by limited theoretical support and statistical properties of clustering analysis remain poorly understood. Alternatively, source attribution methods allow fitting of HIV transmission models and thereby quantify aspects of disease transmission.A simulation study was conducte...
Source: Epidemics - July 11, 2018 Category: Epidemiology Source Type: research
Dynamics and control of infections on social networks of population types
Publication date: June 2018Source: Epidemics, Volume 23Author(s): Brian G. Williams, Christopher DyeAbstractRandom mixing in host populations has been a convenient simplifying assumption in the study of epidemics, but neglects important differences in contact rates within and between population groups. For HIV/AIDS, the assumption of random mixing is inappropriate for epidemics that are concentrated in groups of people at high risk, including female sex workers (FSW) and their male clients (MCF), injecting drug users (IDU) and men who have sex with men (MSM). To find out who transmits infection to whom and how that affects...
Source: Epidemics - July 11, 2018 Category: Epidemiology Source Type: research
Digital Dermatitis in dairy cattle: The contribution of different disease classes to transmission
Publication date: June 2018Source: Epidemics, Volume 23Author(s): Floor Biemans, Piter Bijma, Natasja M. Boots, Mart C.M. de JongAbstractDigital Dermatitis (DD) is a claw disease mainly affecting the hind feet of dairy cattle. Digital Dermatitis is an infectious disease, transmitted via the environment, where the infectious “agent” is a combination of bacteria. The standardized classification for DD lesions developed by Döpfer et al. (1997) and extended by Berry et al. (2012) has six distinct classes: healthy (M0), an active granulomatous area of 0–2 cm (M1), an ulcerative lesion of>2 cm (M2), an ulcerative lesi...
Source: Epidemics - July 11, 2018 Category: Epidemiology Source Type: research
