Real-time forecasting of epidemic trajectories using computational dynamic ensembles
Publication date: Available online 21 December 2019Source: EpidemicsAuthor(s): G. Chowell, R. Luo, K. Sun, K. Roosa, A. Tariq, C. ViboudAbstractForecasting the trajectory of social dynamic processes, such as the spread of infectious diseases, poses significant challenges that call for methods that account for data and model uncertainty. Here we introduce an ensemble model for sequential forecasting that weights a set of plausible models and use a frequentist computational bootstrap approach to evaluate its uncertainty. We demonstrate the feasibility of our approach using simple dynamic differential-equation models and the ...
Source: Epidemics - December 21, 2019 Category: Epidemiology Source Type: research
Dynamic modeling of hepatitis C transmission among people who inject drugs
Publication date: Available online 11 December 2019Source: EpidemicsAuthor(s): Theresa Stocks, Leah J. Martin, Sharon Kühlmann-Berenzon, Tom BrittonAbstractTo reach the WHO goal of hepatitis C elimination, it is essential to identify the number of people unaware of their hepatitis C virus (HCV) infection and to investigate the effect of interventions on the disease transmission dynamics. In many high-income countries, one of the primary routes of HCV transmission is via contaminated needles shared by people who inject drugs (PWIDs). However, substantial underreporting combined with high uncertainty regarding the size of t...
Source: Epidemics - December 11, 2019 Category: Epidemiology Source Type: research
Prospects of toxoplasmosis control by cat vaccination
ConclusionFor attaining elimination of oocyst-originated human infections, only few cats may remain unvaccinated, regardless of the cat-population size, and only a few more cats may remain unvaccinated for reducing infections substantially. Such vaccination coverages can in practice be achieved only when small cat-populations are considered, but in larger cat-populations the large efficacy and vaccination coverage needed are unfeasible. (Source: Epidemics)
Source: Epidemics - December 6, 2019 Category: Epidemiology Source Type: research
Temperature-dependent variation in the extrinsic incubation period elevates the risk of vector-borne disease emergence
Publication date: Available online 6 December 2019Source: EpidemicsAuthor(s): Tsukushi Kamiya, Megan A. Greischar, Kiran Wadhawan, Benjamin Gilbert, Krijn Paaijmans, Nicole MideoAbstractIdentifying ecological drivers of disease transmission is central to understanding disease risks. For vector-borne diseases, temperature is a major determinant of transmission because vital parameters determining the fitness of parasites and vectors are highly temperature-sensitive, including the extrinsic incubation period required for parasites to develop within the vector. Temperature also underlies dramatic differences in the individual...
Source: Epidemics - December 6, 2019 Category: Epidemiology Source Type: research
Epidemiological Impact of Targeted Interventions for People with Diabetes Mellitus on Tuberculosis Transmission in India: Modelling Based Predictions
ConclusionGains can be attained by targeting DM individuals with interventions to reduce TB burden. Most strategies were effective with <50 intervention doses needed to avert one TB disease case, informing key updates of current treatment guidelines. (Source: Epidemics)
Source: Epidemics - December 4, 2019 Category: Epidemiology Source Type: research
Predicting Ebola virus disease risk and the role of African bat birthing
Publication date: Available online 16 November 2019Source: EpidemicsAuthor(s): C. Reed Hranac, Jonathan C. Marshall, Ara Monadjem, David T.S. HaymanAbstractEbola virus disease (EVD) presents a threat to public health throughout equatorial Africa. Despite numerous ‘spillover’ events into humans and apes, the maintenance reservoirs and mechanism of spillover are poorly understood. Evidence suggests fruit bats play a role in both instances, yet data remain sparse and bats exhibit a wide range of life history traits. Here we pool sparse data and use a mechanistic approach to examine how birthing cycles of African fruit bat...
Source: Epidemics - November 17, 2019 Category: Epidemiology Source Type: research
Phylodynamic analysis of HIV-1 subtypes B, C and CRF 02_AG in Senegal
Publication date: Available online 14 November 2019Source: EpidemicsAuthor(s): Fabrícia F. Nascimento, Stefan Baral, Lily Geidelberg, Christinah Mukandavire, Sheree R. Schwartz, Gnilane Turpin, Nguissali Turpin, Daouda Diouf, Nafissatou Leye Diouf, Karleen Coly, Coumba Toure Kane, Cheikh Ndour, Peter Vickerman, Marie-Claude Boily, Erik M. VolzAbstractSurveillance of HIV epidemics in key populations and in developing countries is often challenging due to sparse, incomplete, or low-quality data. Analysis of HIV sequence data can provide an alternative source of information about epidemic history, population structure, and t...
Source: Epidemics - November 14, 2019 Category: Epidemiology Source Type: research
Measles transmission during a large outbreak in California
Publication date: Available online 10 November 2019Source: EpidemicsAuthor(s): Lee Worden, Sarah F. Ackley, Jennifer Zipprich, Kathleen Harriman, Wayne T.A. Enanoria, Rae Wannier, Travis C. PorcoAbstractA large measles outbreak in 2014–2015, linked to Disneyland theme parks, attracted international attention, and led to changes in California vaccine policy. We use dates of symptom onset and known epidemic links for California cases in this outbreak to estimate time-varying transmission in the outbreak, and to estimate generation membership of cases probabilistically. We find that transmission declined significantly durin...
Source: Epidemics - November 11, 2019 Category: Epidemiology Source Type: research
The forecasting of dynamical Ross River virus outbreaks: Victoria, Australia
Publication date: Available online 5 November 2019Source: EpidemicsAuthor(s): Iain S. Koolhof, Katherine B. Gibney, Silvana Bettiol, Michael Charleston, Anke Wiethoelter, Anna-Lena Arnold, Patricia T. Campbell, Peter J. Neville, Phyo. Aung, Tsubasa Shiga, Scott Carver, Simon M. FirestoneAbstractRoss River virus (RRV) is Australia’s most epidemiologically important mosquito-borne disease. During RRV epidemics in the State of Victoria (such as 2010/11 and 2016/17) notifications can account for up to 30% of national RRV notifications. However, little is known about factors which can forecast RRV transmission in Victoria. We...
Source: Epidemics - November 6, 2019 Category: Epidemiology Source Type: research
Desirable BUGS in models of infectious diseases
Publication date: Available online 17 October 2019Source: EpidemicsAuthor(s): Megan Auzenbergs, Carla Correia-Gomes, Theo Economou, Rachel Lowe, Kathleen M O’ReillyAbstractBayesian inference using Gibbs sampling (BUGS) is a set of statistical software that uses Markov chain Monte Carlo (MCMC) methods to estimate almost any specified model. Originally developed in the late 1980s, the software is an excellent introduction to applied Bayesian statistics without the need to write a MCMC sampler. The software is typically used for regression-based analyses, but any models that can be specified using graphical nodes are possib...
Source: Epidemics - October 18, 2019 Category: Epidemiology Source Type: research
Heterogeneous infectiousness in mathematical models of tuberculosis: a systematic review
Publication date: Available online 17 October 2019Source: EpidemicsAuthor(s): Yayehirad A. Melsew, Adeshina I. Adekunle, Allen C. Cheng, Emma S. McBryde, Romain Ragonnet, James M. TrauerAbstractTB mathematical models employ various assumptions and approaches in dealing with the heterogeneous infectiousness of persons with active TB. We reviewed existing approaches and considered the relationship between them and existing epidemiological evidence.We searched the following electronic bibliographic databases from inception to 9 October 2018: MEDLINE, EMBASE, Biosis, Global Health and Scopus. Two investigators extracted data u...
Source: Epidemics - October 18, 2019 Category: Epidemiology Source Type: research
Transmission of and susceptibility to seasonal influenza in Switzerland from 2003 to 2015
The objective of this study was to obtain a detailed picture of the transmission dynamics of seasonal influenza in Switzerland from 2003 to 2015. To this end, we developed a compartmental influenza transmission model taking into account social mixing between different age groups and seasonal forcing. We applied a Bayesian approach using Markov chain Monte Carlo (MCMC) methods to fit the model to the reported incidence of influenza-like-illness (ILI) and virological data from Sentinella, the Swiss Sentinel Surveillance Network. The maximal basic reproduction number, R0, ranged from 1.46 to 1.81 (median). Median estimates of...
Source: Epidemics - October 11, 2019 Category: Epidemiology Source Type: research
Contemporary statistical inference for infectious disease models using Stan
We describe the fitting of a class of epidemic models using Hamiltonian Monte Carlo and variational inference as implemented in the freely available Stan software. We apply the two methods to real data from outbreaks as well as routinely collected observations. Our results suggest that both inference methods are computationally feasible in this context, and show a trade-off between statistical efficiency versus computational speed. The latter appears particularly relevant for real-time applications. (Source: Epidemics)
Source: Epidemics - October 5, 2019 Category: Epidemiology Source Type: research
Game theory of vaccination and depopulation for managing livestock diseases and zoonoses on small-scale farms
The objective of this theoretical study was to elucidate how these behavioral adaptations may affect the epidemiology of highly-pathogenic avian influenza in domestic poultry and the outcome of the implemented control policies. We studied a symmetric population game where the players are broiler poultry farmers at risk of infection and where the between-farms disease transmission is both environmental and mediated by poultry trade. Three types of farmer behaviors were modelled: vaccination, depopulation, and cessation of poultry farming. We found that the transmission level of the disease through trade networks has strong ...
Source: Epidemics - October 4, 2019 Category: Epidemiology Source Type: research
Introduction to particle Markov-chain Monte Carlo for disease dynamics modellers
Publication date: Available online 3 October 2019Source: EpidemicsAuthor(s): Akira Endo, Edwin van Leeuwen, Marc BaguelinAbstractThe particle Markov-chain Monte Carlo (PMCMC) method is a powerful tool to efficiently explore high-dimensional parameter space using time-series data. We illustrate an overall picture of PMCMC with minimal but sufficient theoretical background to support the readers in the field of biomedical/health science to apply PMCMC to their studies. Some working examples of PMCMC applied to infectious disease dynamic models are presented with R code. (Source: Epidemics)
Source: Epidemics - October 4, 2019 Category: Epidemiology Source Type: research
