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Sophie R Meakin, Matt J Keeling
It is increasingly apparent that heterogeneity in the interaction between individuals plays an important role in the dynamics, persistence, evolution and control of infectious diseases. In epidemic modelling two main forms of heterogeneity are commonly considered: spatial heterogeneity due to the segregation of populations and heterogeneity in risk at the same location. The transition from random-mixing to heterogeneous-mixing models is made by incorporating the interaction, or coupling, within and between subpopulations...
August 30, 2018: Epidemics
Sarah E Stansfield, John E Mittler, Geoffrey S Gottlieb, James T Murphy, Deven T Hamilton, Roger Detels, Steven M Wolinsky, Lisa P Jacobson, Joseph B Margolick, Charles R Rinaldo, Joshua T Herbeck, Steven M Goodreau
BACKGROUND: HIV-1 set point viral load (SPVL) is a highly variable trait that influences disease progression and transmission risk. Men who are exclusively insertive (EI) during anal intercourse require more sexual contacts to become infected than exclusively receptive (ER) men. Thus, we hypothesize that EIs are more likely to acquire their viruses from highly infectious partners (i.e., with high SPVLs) and to have higher SPVLs than infected ERs. METHODS: We used a one-generation Bernoulli model, a dynamic network model, and data from the Multicenter AIDS Cohort Study (MACS) to examine whether and under what circumstances MSM differ in SPVL by sexual role...
August 30, 2018: Epidemics
Clara Champagne, Richard Paul, Sowath Ly, Veasna Duong, Rithea Leang, Bernard Cazelles
Dengue 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 Kampong Cham (Cambodia), in which serotypes and asymptomatic infections were documented...
August 29, 2018: Epidemics
M Aldrin, P A Jansen, H Stryhn
The 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 stage-structured, comprising of (i) adult female lice and (ii) other mobile stages of lice...
August 18, 2018: Epidemics
Wayne M Getz, Richard Salter, Oliver Muellerklein, Hyun S Yoon, Krti Tallam
Epidemiological 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 we outline how they can be easily and rapidly constructed using Numerus Model Builder, a graphically-driven coding platform...
July 13, 2018: Epidemics
Julia Reis, Teresa Yamana, Sasikiran Kandula, Jeffrey Shaman
Respiratory syncytial virus (RSV) infections peak during the winter months in the United States, yet the timing, intensity, and onset of these outbreaks vary each year. An RSV vaccine is on the cusp of being released; precise models and accurate forecasts of RSV epidemics may prove vital for planning where and when the vaccine should be deployed. Accurate forecasts with sufficient spatial and temporal resolution could also be used to support the prevention or treatment of RSV infections. Previously, we developed and validated an RSV forecast system at the regional scale in the United States...
July 9, 2018: Epidemics
Jessica Enright, Rowland Raymond Kao
In many populations, the patterns of potentially infectious contacts are transients that can be described as a network with dynamic links. The relative timescales of link and contagion dynamics and the characteristics that drive their tempos can lead to important differences to the static case. Here, we propose some essential nomenclature for their analysis, and then review the relevant literature. 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...
September 2018: Epidemics
Adel Elghafghuf, Raphael Vanderstichel, Sophie St-Hilaire, Henrik Stryhn
Sea lice are marine parasites affecting salmon farms, and are considered one of the most costly pests of the salmon aquaculture industry. Infestations of sea lice on farms significantly increase opportunities for the parasite to spread in the surrounding ecosystem, making control of this pest a challenging issue for salmon producers. The complexity of controlling sea lice on salmon farms requires frequent monitoring of the abundance of different sea lice stages over time. Industry-based data sets of counts of lice are amenable to multivariate time-series data analyses...
September 2018: Epidemics
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 U.S. swine represents one of the best documented emergences of a highly infectious pathogen in the U...
September 2018: Epidemics
Joost H Smid, Victor Garcia, Nicola Low, Catherine H Mercer, Christian L Althaus
Heterosexual partners often differ in age. Integrating realistic patterns of sexual mixing by age into dynamic transmission models has been challenging. The effects of these patterns on the transmission of sexually transmitted infections (STI) including Chlamydia trachomatis (chlamydia), the most common bacterial STI are not well understood. We describe age mixing between new heterosexual partners using age- and sex-specific data about sexual behavior reported by people aged 16-63 years in the 2000 and 2010 British National Surveys of Sexual Attitudes and Lifestyles...
September 2018: Epidemics
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 influenza viruses co-circulated at the same time. However, the epidemic timing differed by influenza (sub)type. Influenza A/H3N2 caused epidemics approximately every 2 years in both cities and tended to alternate with A/H1N1 or B...
September 2018: Epidemics
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 of how a pandemic would spread in the UK...
September 2018: Epidemics
Thomas M Lietman, Lee Worden, Fengchen Liu, Travis C Porco
Mathematical 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 2008-2013, goodness-of-fit testing was unable to exclude the geometric, and the shape parameter of the best fit negative binomial distribution was close to unity (0...
September 2018: Epidemics
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 algorithms based on estimating reproductive numbers...
September 2018: Epidemics
R J Orton, M Deason, P R Bessell, D M Green, R R Kao, L C M Salvador
Bovine 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 specific Mycobacterium bovis genotypes...
September 2018: Epidemics
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 Reed
Accurate 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 Service Regions. Forecasted targets for the 2014-15 challenge were the onset week, peak week, and peak intensity of the season and the weekly percent of outpatient visits due to influenza-like illness (ILI) 1-4 weeks in advance. We used a logarithmic scoring rule to score the weekly forecasts, averaged the scores over an evaluation period, and then exponentiated the resulting logarithmic score...
September 2018: Epidemics
Peter F M Teunis, Axel Bonačić Marinović, David R Tribble, Chad K Porter, Arno Swart
Data 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. High susceptibility to infection with C. jejuni was found in a joint analysis of outbreaks and challenge studies...
September 2018: Epidemics
Van Kinh Nguyen, César Parra-Rojas, Esteban A Hernandez-Vargas
From August to November 2017, Madagascar endured an outbreak of plague. A total of 2417 cases of plague were confirmed, causing a death toll of 209. Public health intervention efforts were introduced and successfully stopped the epidemic at the end of November. The plague, however, is endemic in the region and occurs annually, posing the risk of future outbreaks. To understand the plague transmission, we collected real-time data from official reports, described the outbreak's characteristics, and estimated transmission parameters using statistical and mathematical models...
June 1, 2018: Epidemics
Sarah Tan, Susanna Makela, Daliah Heller, Kevin Konty, Sharon Balter, Tian Zheng, James H Stark
Existing 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 associated uncertainty. Our approach improves on previous estimates by explicitly accounting for injecting drug use and including data from high-risk subpopulations such as the incarcerated, and is more inclusive, utilizing ten NYC data sources...
June 2018: Epidemics
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 Napp
In 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 bTB from the herds already infected. Here, we developed a compartmental stochastic model to simulate bTB within-herd transmission, fed it with epidemiological data from 22 herds (obtained from a previous work) and carried out parameter inference using Approximate Bayesian Computing methods We also estimated the "Within-herd transmission potential Number" (Rh ), i...
June 2018: Epidemics
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