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Epidemics

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https://www.readbyqxmd.com/read/30446431/fogarty-international-center-collaborative-networks-in-infectious-disease-modeling-lessons-learnt-in-research-and-capacity-building
#1
REVIEW
Martha I Nelson, James O Lloyd-Smith, Lone Simonsen, Andrew Rambaut, Edward C Holmes, Gerardo Chowell, Mark A Miller, David J Spiro, Bryan Grenfell, Cécile Viboud
Due to a combination of ecological, political, and demographic factors, the emergence of novel pathogens has been increasingly observed in animals and humans in recent decades. Enhancing global capacity to study and interpret infectious disease surveillance data, and to develop data-driven computational models to guide policy, represents one of the most cost-effective, and yet overlooked, ways to prepare for the next pandemic. Epidemiological and behavioral data from recent pandemics and historic scourges have provided rich opportunities for validation of computational models, while new sequencing technologies and the 'big data' revolution present new tools for studying the epidemiology of outbreaks in real time...
October 23, 2018: Epidemics
https://www.readbyqxmd.com/read/30344024/the-impact-of-influenza-vaccination-on-infection-hospitalisation-and-mortality-in-the-netherlands-between-2003-and-2015
#2
J A Backer, J Wallinga, A Meijer, G A Donker, W van der Hoek, M van Boven
Influenza epidemics annually cause substantial morbidity and mortality. For this reason, vaccination is offered yearly to persons with an elevated risk for complications. Assessments of the impact of vaccination are, however, hampered by year-to-year variation in epidemic size and vaccine effectiveness. We estimate the impact of the current vaccination programme comparing simulations with vaccination to counterfactual simulations without vaccination. The simulations rely on an age- and risk-structured transmission model that tracks the build-up and loss of immunity over successive seasons, and that allows the vaccine match to vary between seasons...
October 11, 2018: Epidemics
https://www.readbyqxmd.com/read/30327253/geographic-transmission-hubs-of-the-2009-influenza-pandemic-in-the-united-states
#3
Stephen M Kissler, Julia R Gog, Cécile Viboud, Vivek Charu, Ottar N Bjørnstad, Lone Simonsen, Bryan T Grenfell
A key issue in infectious disease epidemiology is to identify and predict geographic sites of epidemic establishment that contribute to onward spread, especially in the context of invasion waves of emerging pathogens. Conventional wisdom suggests that these sites are likely to be in densely-populated, well-connected areas. For pandemic influenza, however, epidemiological data have not been available at a fine enough geographic resolution to test this assumption. Here, we make use of fine-scale influenza-like illness incidence data derived from electronic medical claims records gathered from 834 3-digit ZIP (postal) codes across the US to identify the key geographic establishment sites, or "hubs", of the autumn wave of the 2009 A/H1N1pdm influenza pandemic in the United States...
October 10, 2018: Epidemics
https://www.readbyqxmd.com/read/30213654/correlations-between-stochastic-epidemics-in-two-interacting-populations
#4
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
https://www.readbyqxmd.com/read/30193771/sexual-role-and-hiv-1-set-point-viral-load-among-men-who-have-sex-with-men
#5
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
https://www.readbyqxmd.com/read/30249390/patterns-of-seasonal-influenza-activity-in-u-s-core-based-statistical-areas-described-using-prescriptions-of-oseltamivir-in-medicare-claims-data
#6
F Scott Dahlgren, David K Shay, Hector S Izurieta, Richard A Forshee, Michael Wernecke, Yoganand Chillarige, Yun Lu, Jeffrey A Kelman, Carrie Reed
Using 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 from 45,888 in 2011-2012 to 380,745 in 2014-2015. For each season, the peak weekly number of prescriptions correlated with the total number of prescriptions (Pearson's r ≥ 0...
August 29, 2018: Epidemics
https://www.readbyqxmd.com/read/30206040/dengue-modeling-in-rural-cambodia-statistical-performance-versus-epidemiological-relevance
#7
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
https://www.readbyqxmd.com/read/30054196/identifying-human-encounters-that-shape-the-transmission-of-streptococcus-pneumoniae-and-other-acute-respiratory-infections
#8
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 individuals who took part in a survey in South-West Uganda. We found that the frequency of physical (i.e. skin-to-skin), long (≥1 h) and household contacts - which capture some measure of close (i...
December 2018: Epidemics
https://www.readbyqxmd.com/read/29884470/kernel-density-estimation-and-approximate-bayesian-computation-for-flexible-epidemiological-model-fitting-in-python
#9
Michael A Irvine, T Déirdre Hollingsworth
Fitting 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 tolerance scheme...
December 2018: Epidemics
https://www.readbyqxmd.com/read/29880306/tuberculosis-outbreak-investigation-using-phylodynamic-analysis
#10
Denise Kühnert, Mireia Coscolla, Daniela Brites, David Stucki, John Metcalfe, Lukas Fenner, Sebastien Gagneux, Tanja Stadler
The fast evolution of pathogenic viruses has allowed for the development of phylodynamic approaches that extract information about the epidemiological characteristics of viral genomes. Thanks to advances in whole genome sequencing, they can be applied to slowly evolving bacterial pathogens like Mycobacterium tuberculosis. 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...
December 2018: Epidemics
https://www.readbyqxmd.com/read/29853411/modelling-the-global-spread-of-diseases-a-review-of-current-practice-and-capability
#11
REVIEW
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 parameterization; model validation data...
December 2018: Epidemics
https://www.readbyqxmd.com/read/29907403/epidemics-on-dynamic-networks
#12
REVIEW
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
https://www.readbyqxmd.com/read/29685498/using-state-space-models-to-predict-the-abundance-of-juvenile-and-adult-sea-lice-on-atlantic-salmon
#13
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
https://www.readbyqxmd.com/read/29673815/role-of-animal-movement-and-indirect-contact-among-farms-in-transmission-of-porcine-epidemic-diarrhea-virus
#14
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
https://www.readbyqxmd.com/read/29655934/age-difference-between-heterosexual-partners-in-britain-implications-for-the-spread-of-chlamydia-trachomatis
#15
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
https://www.readbyqxmd.com/read/29576517/transmission-dynamics-of-influenza-in-two-major-cities-of-uganda
#16
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
https://www.readbyqxmd.com/read/29576516/contagion-the-bbc-four-pandemic-the-model-behind-the-documentary
#17
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
https://www.readbyqxmd.com/read/29567064/the-distribution-of-district-level-leprosy-incidence-in-india-is-geometric-stable-consistent-with-subcriticality
#18
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
https://www.readbyqxmd.com/read/29567063/robust-qualitative-estimation-of-time-varying-contact-rates-in-uncertain-epidemics
#19
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
https://www.readbyqxmd.com/read/29548927/identifying-genotype-specific-elevated-risk-areas-and-associated-herd-risk-factors-for-bovine-tuberculosis-spread-in-british-cattle
#20
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
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