Kernel-density estimation and approximate Bayesian computation for flexible epidemiological model fitting in Python
Publication date: Available online 26 May 2018 Source:Epidemics Author(s): Michael A. Irvine, T. Déirdre Hollingsworth (Source: Epidemics)
Source: Epidemics - May 26, 2018 Category: Epidemiology Source Type: research
Tuberculosis outbreak investigation using phylodynamic analysis
In this study, we investigate and compare the epidemiological dynamics underlying twoM. tuberculosisoutbreaks 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 phylogeneticM. tuberculosisLineage 4. The second outbreak was caused by a multidrug-resistant (MDR) strain ofLineage2, imported from the Wat Tham...
Source: Epidemics - May 22, 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 2018 Source:Epidemics Author(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 Edmunds Although 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...
Source: Epidemics - May 19, 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 2018 Source:Epidemics Author(s): Roxanne Beauclair, Niel Hens, Wim Delva Background Age-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. Methods We 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 ...
Source: Epidemics - May 18, 2018 Category: Epidemiology Source Type: research
Modelling the global spread of diseases: a review of current practice and capability
Publication date: Available online 18 May 2018 Source:Epidemics Author(s): Caroline E. Walters, Margaux M.I. Meslé, Ian M. Hall Mathematical 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 param...
Source: Epidemics - May 18, 2018 Category: Epidemiology Source Type: research
Using serological studies to reconstruct the history of bluetongue epidemic in French cattle under successive vaccination campaigns
Publication date: Available online 17 May 2018 Source:Epidemics Author(s): Noémie Courtejoie, Henrik Salje, Benoît Durand, Gina Zanella, Simon Cauchemez Bluetongue virus is a vector-borne pathogen affecting ruminants that has caused major epidemics in France. Reconstructing the history of bluetongue in French cattle under control strategies such as vaccination has been hampered by the high level of sub-clinical infection, incomplete case data and poor understanding of vaccine uptake over time and space. To tackle these challenges, we used three age-structured serological surveys carried out in cattle (N = 22,3...
Source: Epidemics - May 17, 2018 Category: Epidemiology Source Type: research
Concurrency of Partnerships, Consistency with Data, and Control of Sexually Transmitted Infections
Publication date: Available online 14 May 2018 Source:Epidemics Author(s): Trystan Leng, Matt J. Keeling Sexually transmitted infections (STIs) are a globally increasing public health problem. Mathematical models, carefully matched to available epidemiological and behavioural data, have an important role to play in predicting the action of control measures. Here, we explore the effect of concurrent sexual partnerships on the control of a generic STI with susceptible-infected-susceptible dynamics. Concurrency refers to being in more than one sexual partnership at the same time, and is difficult to measure accurately. We...
Source: Epidemics - May 15, 2018 Category: Epidemiology Source Type: research
A model for leptospire dynamics and control in the Norway rat (Rattus norvegicus) the reservoir host in urban slum environments
Publication date: Available online 5 May 2018 Source:Epidemics Author(s): Amanda Minter, Peter J. Diggle, Federico Costa, James Childs, Albert I. Ko, Mike Begon Leptospirosis is a zoonosis that humans can contract via contact with animal reservoirs directly or with water contaminated with their urine. The primary reservoir of pathogenic leptospires within urban slum environments is the Norway rat (Rattus norvegicus). Motivated by the annual outbreaks of human leptospirosis in slum urban settings, the within population infection dynamics of the Norway rat were investigated in Pau da Lima, an community in Salvador, B...
Source: Epidemics - May 6, 2018 Category: Epidemiology Source Type: research
Epidemics on dynamic networks
We describe recent advances in they apply to infection processes, considering all of the methods used to record, measure and analyse them, and their implications for disease transmission. Finally, we outline some key challenges and opportunities in the field. (Source: Epidemics)
Source: Epidemics - April 28, 2018 Category: Epidemiology Source Type: research
Role of animal movement and indirect contact among farms in transmission of porcine epidemic diarrhea virus
Publication date: Available online 12 April 2018 Source:Epidemics Author(s): Kimberly VanderWaal, Andres Perez, Montse Torremorrell, Robert M. Morrison, Meggan Craft Epidemiological models of the spread of pathogens in livestock populations primarily focus on direct contact between farms based on animal movement data, and in some cases, local spatial spread based on proximity between premises. The roles of other types of indirect contact among farms is rarely accounted for. In addition, data on animal movements is seldom available in the United States. However, the spread of porcine epidemic diarrhea virus (PEDv) in...
Source: Epidemics - April 12, 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 - April 11, 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 - March 31, 2018 Category: Epidemiology Source Type: research
Contagion! The BBC Four Pandemic – The model behind the documentary
Publication date: Available online 22 March 2018 Source:Epidemics Author(s): Petra Klepac, Stephen Kissler, Julia Gog To 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 - March 22, 2018 Category: Epidemiology Source Type: research
Transmission Dynamics of Influenza in Two Major Cities of Uganda
Publication date: Available online 19 March 2018 Source:Epidemics Author(s): Wan Yang, Matthew J. Cummings, Barnabas Bakamutumaho, John Kayiwa, Nicholas Owor, Barbara Namagambo, Timothy Byaruhanga, Julius J. Lutwama, Max R. O’Donnell, Jeffrey Shaman In 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 influ...
Source: Epidemics - March 19, 2018 Category: Epidemiology Source Type: research
Robust qualitative estimation of time-varying contact rates in uncertain epidemics
Publication date: Available online 15 March 2018 Source:Epidemics Author(s): Marco Tulio Angulo, Jorge X. Velasco-Hernandez We 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 a...
Source: Epidemics - March 16, 2018 Category: Epidemiology Source Type: research
