Enhancing Bayesian risk prediction for epidemics using contact tracing

Contact tracing data collected from disease outbreaks has received relatively little attention in the epidemic modelling literature because it is thought to be unreliable: infection sources might be wrongly attributed, or data might be missing due to resource contraints in the questionnaire exercise. Nevertheless, these data might provide a rich source of information on disease transmission rate. This paper presents novel methodology for combining contact tracing data with rate-based contact network data to improve posterior precision, and therefore predictive accuracy. We present an advancement in Bayesian inference for epidemics that assimilates these data, and is robust to partial contact tracing. Using a simulation study based on the British poultry industry, we show how the presence of contact tracing data improves posterior predictive accuracy, and can directly inform a more effective control strategy.Comment: 40 pages, 9 figures. Submitted to Biostatistic

A Hidden Markov Model for Analysis of Frontline Veterinary Data for Emerging Zoonotic Disease Surveillance

Surveillance systems tracking health patterns in animals have potential for early warning of infectious disease in humans, yet there are many challenges that remain before this can be realized. Specifically, there remains the challenge of detecting early warning signals for diseases that are not known or are not part of routine surveillance for named diseases. This paper reports on the development of a hidden Markov model for analysis of frontline veterinary sentinel surveillance data from Sri Lanka. Field veterinarians collected data on syndromes and diagnoses using mobile phones. A model for submission patterns accounts for both sentinel-related and disease-related variability. Models for commonly reported cattle diagnoses were estimated separately. Region-specific weekly average prevalence was estimated for each diagnoses and partitioned into normal and abnormal periods. Visualization of state probabilities was used to indicate areas and times of unusual disease prevalence. The analysis suggests that hidden Markov modelling is a useful approach for surveillance datasets from novel populations and/or having little historical baselines

Disease surveillance using a hidden Markov model

<p>Abstract</p> <p>Background</p> <p>Routine surveillance of disease notification data can enable the early detection of localised disease outbreaks. Although hidden Markov models (HMMs) have been recognised as an appropriate method to model disease surveillance data, they have been rarely applied in public health practice. We aimed to develop and evaluate a simple flexible HMM for disease surveillance which is suitable for use with sparse small area count data and requires little baseline data.</p> <p>Methods</p> <p>A Bayesian HMM was designed to monitor routinely collected notifiable disease data that are aggregated by residential postcode. Semi-synthetic data were used to evaluate the algorithm and compare outbreak detection performance with the established Early Aberration Reporting System (EARS) algorithms and a negative binomial cusum.</p> <p>Results</p> <p>Algorithm performance varied according to the desired false alarm rate for surveillance. At false alarm rates around 0.05, the cusum-based algorithms provided the best overall outbreak detection performance, having similar sensitivity to the HMMs and a shorter average time to detection. At false alarm rates around 0.01, the HMM algorithms provided the best overall outbreak detection performance, having higher sensitivity than the cusum-based Methods and a generally shorter time to detection for larger outbreaks. Overall, the 14-day HMM had a significantly greater area under the receiver operator characteristic curve than the EARS C3 and 7-day negative binomial cusum algorithms.</p> <p>Conclusion</p> <p>Our findings suggest that the HMM provides an effective method for the surveillance of sparse small area notifiable disease data at low false alarm rates. Further investigations are required to evaluation algorithm performance across other diseases and surveillance contexts.</p

FluDetWeb: an interactive web-based system for the early detection of the onset of influenza epidemics

<p>Abstract</p> <p>Background</p> <p>The early identification of influenza outbreaks has became a priority in public health practice. A large variety of statistical algorithms for the automated monitoring of influenza surveillance have been proposed, but most of them require not only a lot of computational effort but also operation of sometimes not-so-friendly software.</p> <p>Results</p> <p>In this paper, we introduce <monospace>FluDetWeb</monospace>, an implementation of a prospective influenza surveillance methodology based on a client-server architecture with a thin (web-based) client application design. Users can introduce and edit their own data consisting of a series of weekly influenza incidence rates. The system returns the probability of being in an epidemic phase (via e-mail if desired). When the probability is greater than 0.5, it also returns the probability of an increase in the incidence rate during the following week. The system also provides two complementary graphs. This system has been implemented using statistical free-software (ℝ and WinBUGS), a web server environment for Java code (<it>Tomcat</it>) and a software module created by us (<it>Rdp</it>) responsible for managing internal tasks; the software package <it>MySQL </it>has been used to construct the database management system. The implementation is available on-line from: <url>http://www.geeitema.org/meviepi/fludetweb/</url>.</p> <p>Conclusion</p> <p>The ease of use of <monospace>FluDetWeb</monospace> and its on-line availability can make it a valuable tool for public health practitioners who want to obtain information about the probability that their system is in an epidemic phase. Moreover, the architecture described can also be useful for developers of systems based on computationally intensive methods.</p

Bayesian temporal and spatio-temporal Markov switching models for the detection of influenza outbreaks

Influenza is a disease which affects millions of people every year and causes hundreds of thousends of deads every year. This disease causes substantial direct and indirect costs every year. The influenza epidemic have a particular behavior which shapes the statistical methods for their detection. Seasonal epidemics happen virtually every year in the temperate parts of the globe during the cold months and extend throughout whole regions, countries and even continents. Besides the seasonal epidemics, some nonseasonal epidemics can be observed at unexpected times, usually caused by strains which jump the barrier between animals and humans, as happened with the well known Swine Flu epidemic, which caused great alarm in 2009. Several statistical methods have been proposed for the detection of outbreaks of diseases and, in particular, for influenza outbreaks. A reduced version of the review present in this thesis has been published in REVSTAT-Statistical Journal by Amorós et al. in 2015. An interesting tool for the modeling of statistical methods for the detection of influenza outbreaks is the use of Markov switching models, where latent variables are paired with the observations, indicating the epidemic or endemic phase. Two different models are applied to the data according to the value of the latent variable. The latent variables are temporally linked through a Markov chain. The observations are also conditionally dependent on their temporal or spatio-temporal neighbors. Models using this tool can offer a probability of being in epidemic as an outcome instead of just a ‘yes’ or ‘no’. Bayesian paradigm offers an interesting framework where the outcomes can be interpreted as probability distributions. Also, inference can be done over complex hierarchical models, as usually the Markov switching models are. This research offer two extensions of the model proposed by Martinez-Beneito et al. in 2008, published in Statistics in Medicine. The first proposal is a framework of Poison Markov switching models over the counts. This proposal has been published in Statistical Methods in Medical Research by Conesa et al. in 2015. In this proposal, the counts are modeled through a Poisson distribution, and the mean of these counts is related to the rates through the population. Then, the rates are modeled through a Normal distribution. The the mean and variance of the rates depend on whether we are in the epidemic or nonepidemic phase for each week. The latent variables which determine the epidemic phase are modeled through a hidden Markov chain. The mean and the variance on the epidemic phase is considered to be larger than the ones on the endemic phase. Different degrees of temporal dependency of the mean of the data can be defined. A first option is be to consider the rates conditionally independent. A second option is to consider that every observation is conditionally dependent on the previous observation through an autoregressive process of order 1. Higher orders of dependency can be defined, but we limited our framework of models to an autoregressive process of order 2 to avoid unnecessary complexity, as no big changes in the outcome were appreciated using higher orders of autocorrelation. The application of this framework of methods over several data bases showed that this proposal outperforms other methodologies present in the literature. It also stresses several difficulties in the process of evaluation of statistical methods for the detection of influenza outbreaks. The second proposal of this research is a spatio-temporal Markov switching model over the differentiated rates, which are considered to follow a normal distribution, with mean and variance parameters dependent on the epidemic state. The latent variables are modeled in the same way as in the temporal proposal, but having one conditionally independent hidden Markov chain for each of the locations. The variance of the endemic phase is also considered to be lower than that of the epidemic phase. Three components are defined for the mean of the differentiated rates: First of all, a common term for all the regions for each time is set in both the endemic and epidemic mean. These terms are defined as two random effects, with mean zero and a higher variance for the epidemic phase. The variances of these random effects are linked to those of the likelihood to avoid problems of identifiability. An autoregressive term for each location is also defined for the epidemic term, as it is expected that from the begining of the epidemic until the peak we observe similar positive jumps and from the peak to the end of the epidemic we observe similar negative jumps. An intrinsic CAR structure is also defined for the epidemic mean, considering that the epidemic can spread to neighbor regions which will have similar epidemic increases of the rates. This proposal has been applied over the United States Google Flu Trends data from 2007 to 2013 for the 48 spatially connected states plus Washington D.C. The comparison of the model with several simplifications and variations has stressed the necessity of several of the assumptions made during the modeling process

Enhancing the monitoring of fallen stock at different hierarchical administrative levels: an illustration on dairy cattle from regions with distinct husbandry, demographical and climate traits

Background: The automated collection of non-specific data from livestock, combined with techniques for data mining and time series analyses, facilitates the development of animal health syndromic surveillance (AHSyS). An example of AHSyS approach relates to the monitoring of bovine fallen stock. In order to enhance part of the machinery of a complete syndromic surveillance system, the present work developed a novel approach for modelling in near real time multiple mortality patterns at different hierarchical administrative levels. To illustrate its functionality, this system was applied to mortality data in dairy cattle collected across two Spanish regions with distinct demographical, husbandry, and climate conditions. Results: The process analyzed the patterns of weekly counts of fallen dairy cattle at different hierarchical administrative levels across two regions between Jan-2006 and Dec-2013 and predicted their respective expected counts between Jan-2014 and Jun- 2015. By comparing predicted to observed data, those counts of fallen dairy cattle that exceeded the upper limits of a conventional 95% predicted interval were identified as mortality peaks. This work proposes a dynamic system that combines hierarchical time series and autoregressive integrated moving average models (ARIMA). These ARIMA models also include trend and seasonality for describing profiles of weekly mortality and detecting aberrations at the region, province, and county levels (spatial aggregations). Software that fitted the model parameters was built using the R statistical packages. Conclusions: The work builds a novel tool to monitor fallen stock data for different geographical aggregations and can serve as a means of generating early warning signals of a health problem. This approach can be adapted to other types of animal health data that share similar hierarchical structures.info:eu-repo/semantics/publishedVersio