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Open accessJournal ArticleDOI: 10.1371/JOURNAL.PMED.1003542

Probabilistic seasonal dengue forecasting in Vietnam: A modelling study using superensembles.

04 Mar 2021-PLOS Medicine (Public Library of Science (PLoS))-Vol. 18, Iss: 3
Abstract: Background With enough advanced notice, dengue outbreaks can be mitigated. As a climate-sensitive disease, environmental conditions and past patterns of dengue can be used to make predictions about future outbreak risk. These predictions improve public health planning and decision-making to ultimately reduce the burden of disease. Past approaches to dengue forecasting have used seasonal climate forecasts, but the predictive ability of a system using different lead times in a year-round prediction system has been seldom explored. Moreover, the transition from theoretical to operational systems integrated with disease control activities is rare. Methods and findings We introduce an operational seasonal dengue forecasting system for Vietnam where Earth observations, seasonal climate forecasts, and lagged dengue cases are used to drive a superensemble of probabilistic dengue models to predict dengue risk up to 6 months ahead. Bayesian spatiotemporal models were fit to 19 years (2002-2020) of dengue data at the province level across Vietnam. A superensemble of these models then makes probabilistic predictions of dengue incidence at various future time points aligned with key Vietnamese decision and planning deadlines. We demonstrate that the superensemble generates more accurate predictions of dengue incidence than the individual models it incorporates across a suite of time horizons and transmission settings. Using historical data, the superensemble made slightly more accurate predictions (continuous rank probability score [CRPS] = 66.8, 95% CI 60.6-148.0) than a baseline model which forecasts the same incidence rate every month (CRPS = 79.4, 95% CI 78.5-80.5) at lead times of 1 to 3 months, albeit with larger uncertainty. The outbreak detection capability of the superensemble was considerably larger (69%) than that of the baseline model (54.5%). Predictions were most accurate in southern Vietnam, an area that experiences semi-regular seasonal dengue transmission. The system also demonstrated added value across multiple areas compared to previous practice of not using a forecast. We use the system to make a prospective prediction for dengue incidence in Vietnam for the period May to October 2020. Prospective predictions made with the superensemble were slightly more accurate (CRPS = 110, 95% CI 102-575) than those made with the baseline model (CRPS = 125, 95% CI 120-168) but had larger uncertainty. Finally, we propose a framework for the evaluation of probabilistic predictions. Despite the demonstrated value of our forecasting system, the approach is limited by the consistency of the dengue case data, as well as the lack of publicly available, continuous, and long-term data sets on mosquito control efforts and serotype-specific case data. Conclusions This study shows that by combining detailed Earth observation data, seasonal climate forecasts, and state-of-the-art models, dengue outbreaks can be predicted across a broad range of settings, with enough lead time to meaningfully inform dengue control. While our system omits some important variables not currently available at a subnational scale, the majority of past outbreaks could be predicted up to 3 months ahead. Over the next 2 years, the system will be prospectively evaluated and, if successful, potentially extended to other areas and other climate-sensitive disease systems.

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5 results found


Open accessJournal ArticleDOI: 10.12688/WELLCOMEOPENRES.17263.1
Marc Choisy1, Angela McBride2, Angela McBride1, Mary Chambers1  +28 moreInstitutions (10)
18 Oct 2021-
Abstract: This article summarises a recent virtual meeting organised by the Oxford University Clinical Research Unit in Vietnam on the topic of climate change and health, bringing local partners, faculty and external collaborators together from across the Wellcome and Oxford networks. Attendees included invited local and global climate scientists, clinicians, modelers, epidemiologists and community engagement practitioners, with a view to setting priorities, identifying synergies and fostering collaborations to help define the regional climate and health research agenda. In this summary paper, we outline the major themes and topics that were identified and what will be needed to take forward this research for the next decade. We aim to take a broad, collaborative approach to including climate science in our current portfolio where it touches on infectious diseases now, and more broadly in our future research directions. We will focus on strengthening our research portfolio on climate-sensitive diseases, and supplement this with high quality data obtained from internal studies and external collaborations, obtained by multiple methods, ranging from traditional epidemiology to innovative technology and artificial intelligence and community-led research. Through timely agenda setting and involvement of local stakeholders, we aim to help support and shape research into global heating and health in the region.

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Topics: Community engagement (51%)

Open accessJournal ArticleDOI: 10.1016/S2542-5196(21)00141-8
Caitlin Pley1, Megan Evans2, Rachel Lowe3, Hugh Montgomery4  +1 moreInstitutions (5)
Abstract: Vector-borne diseases are particularly sensitive to changes in weather and climate. Timely warnings from surveillance systems can help to detect and control outbreaks of infectious disease, facilitate effective management of finite resources, and contribute to knowledge generation, response planning, and resource prioritisation in the long term, which can mitigate future outbreaks. Technological and digital innovations have enabled the incorporation of climatic data into surveillance systems, enhancing their capacity to predict trends in outbreak prevalence and location. Advance notice of the risk of an outbreak empowers decision makers and communities to scale up prevention and preparedness interventions and redirect resources for outbreak responses. In this Viewpoint, we outline important considerations in the advent of new technologies in disease surveillance, including the sustainability of innovation in the long term and the fundamental obligation to ensure that the communities that are affected by the disease are involved in the design of the technology and directly benefit from its application.

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Topics: Disease surveillance (58%), Preparedness (50%)

Open accessPosted ContentDOI: 10.1101/2020.10.21.20210948
Gal Koplewitz1, Fred Lu2, Fred Lu3, Cesar Leonardo Clemente1  +3 moreInstitutions (3)
25 Oct 2020-medRxiv
Abstract: The dengue virus affects millions of people every year worldwide, causing large epidemic outbreaks that disrupt people’s lives and severely strain healthcare systems. In the absence of a reliable vaccine against it or an effective treatment to manage the illness in humans, most efforts to combat dengue infections have focused on preventing its vectors, mainly the Aedes aegypti mosquito, from flourishing across the world. These mosquito-control strategies need reliable disease activity surveillance systems to be deployed. Despite significant efforts to estimate dengue incidence using a variety of data sources and methods, little work has been done to understand the relative contribution of the different data sources to improved prediction. Additionally, scholarship on the topic had initially focused on prediction systems at the national- and state-levels, and much remains to be done at the finer spatial resolutions at which health policy interventions often occur. We develop a methodological framework to assess and compare dengue incidence estimates at the city level, and evaluate the performance of a collection of models on 20 different cities in Brazil. The data sources we use towards this end are weekly incidence counts from prior years (seasonal autoregressive terms), weekly-aggregated weather variables, and real-time internet search data. We find that both random forest-based models and LASSO regression-based models effectively leverage these multiple data sources to produce accurate predictions, and that while the performance between them is comparable on average, the former method produces fewer extreme outliers, and can thus be considered more robust. For real-time predictions that assume long delays (6-8 weeks) in the availability of epidemiological data, we find that real-time internet search data are the strongest predictors of dengue incidence, whereas for predictions that assume short delays (1-3 weeks), in which the error rate is halved (as measured by relative RMSE), short-term and seasonal autocorrelation are the dominant predictors. Despite the difficulties inherent to city-level prediction, our framework achieves meaningful and actionable estimates across cities with different demographic, geographic and epidemic characteristics. Author Summary As the incidence of infectious diseases like dengue continues to increase throughout the world, tracking their spread in real time poses a significant challenge to local and national health authorities. Accurate incidence data are often difficult to obtain as outbreaks emerge and unfold, both due the partial reach of serological surveillance (especially in rural areas), and due to delays in reporting, which result in post-hoc adjustments to what should have been real-time data. Thus, a range of ‘nowcasting’ tools have been developed to estimate disease trends, using different mathematical and statistical methodologies to fill the temporal data gap. Over the past several years, researchers have investigated how to best incorporate internet search data into predictive models, since these can be obtained in real-time. Still, most such models have been regression-based, and have tended to underperform in cases when epidemiological data are only available after long reporting delays. Moreover, in tropical countries, attention has increasingly turned from testing and applying models at the national level to models at higher spatial resolutions, such as states and cities. Here, we develop machine learning models based on both LASSO regression and on random forest ensembles, and proceed to apply and compare them across 20 cities in Brazil. We find that our methodology produces meaningful and actionable disease estimates at the city level with both underlying model classes, and that the two perform comparably across most metrics, although the ensemble method produces fewer outliers. We also compare model performance and the relative contribution of different data sources across diverse geographic, demographic and epidemic conditions.

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Open accessJournal ArticleDOI: 10.3390/IJERPH182212108
Abstract: The present analysis uses the data of confirmed incidence of dengue cases in the metropolitan region of Panama from 1999 to 2017 and climatic variables (air temperature, precipitation, and relative humidity) during the same period to determine if there exists a correlation between these variables. In addition, we compare the predictive performance of two regression models (SARIMA, SARIMAX) and a recurrent neural network model (RNN-LSTM) on the dengue incidence series. For this data from 1999–2014 was used for training and the three subsequent years of incidence 2015–2017 were used for prediction. The results show a correlation coefficient between the climatic variables and the incidence of dengue were low but statistical significant. The RMSE and MAPE obtained for the SARIMAX and RNN-LSTM models were 25.76, 108.44 and 26.16, 59.68, which suggest that any of these models can be used to predict new outbreaks. Although, it can be said that there is a limited role of climatic variables in the outputs the models. The value of this work is that it helps understand the behaviour of cases in a tropical setting as is the Metropolitan Region of Panama City, and provides the basis needed for a much needed early alert system for the region.

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Topics: Regression analysis (53%)

Open accessJournal ArticleDOI: 10.1371/JOURNAL.PMED.1003793
19 Oct 2021-PLOS Medicine
Abstract: BACKGROUND: The importance of infectious disease epidemic forecasting and prediction research is underscored by decades of communicable disease outbreaks, including COVID-19. Unlike other fields of medical research, such as clinical trials and systematic reviews, no reporting guidelines exist for reporting epidemic forecasting and prediction research despite their utility. We therefore developed the EPIFORGE checklist, a guideline for standardized reporting of epidemic forecasting research. METHODS AND FINDINGS: We developed this checklist using a best-practice process for development of reporting guidelines, involving a Delphi process and broad consultation with an international panel of infectious disease modelers and model end users. The objectives of these guidelines are to improve the consistency, reproducibility, comparability, and quality of epidemic forecasting reporting. The guidelines are not designed to advise scientists on how to perform epidemic forecasting and prediction research, but rather to serve as a standard for reporting critical methodological details of such studies. CONCLUSIONS: These guidelines have been submitted to the EQUATOR network, in addition to hosting by other dedicated webpages to facilitate feedback and journal endorsement.

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Topics: Communicable disease (55%), Delphi method (54%), Systematic review (52%)
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81 results found


Open accessJournal ArticleDOI: 10.1038/NATURE12060
Samir Bhatt1, Peter W. Gething1, Oliver J. Brady1, Jane P. Messina1  +19 moreInstitutions (9)
25 Apr 2013-Nature
Abstract: Dengue is a systemic viral infection transmitted between humans by Aedes mosquitoes. For some patients, dengue is a life-threatening illness. There are currently no licensed vaccines or specific therapeutics, and substantial vector control efforts have not stopped its rapid emergence and global spread. The contemporary worldwide distribution of the risk of dengue virus infection and its public health burden are poorly known. Here we undertake an exhaustive assembly of known records of dengue occurrence worldwide, and use a formal modelling framework to map the global distribution of dengue risk. We then pair the resulting risk map with detailed longitudinal information from dengue cohort studies and population surfaces to infer the public health burden of dengue in 2010. We predict dengue to be ubiquitous throughout the tropics, with local spatial variations in risk influenced strongly by rainfall, temperature and the degree of urbanization. Using cartographic approaches, we estimate there to be 390 million (95% credible interval 284-528) dengue infections per year, of which 96 million (67-136) manifest apparently (any level of disease severity). This infection total is more than three times the dengue burden estimate of the World Health Organization. Stratification of our estimates by country allows comparison with national dengue reporting, after taking into account the probability of an apparent infection being formally reported. The most notable differences are discussed. These new risk maps and infection estimates provide novel insights into the global, regional and national public health burden imposed by dengue. We anticipate that they will provide a starting point for a wider discussion about the global impact of this disease and will help to guide improvements in disease control strategies using vaccine, drug and vector control methods, and in their economic evaluation.

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Topics: Dengue vaccine (69%), 2009 Bolivian dengue fever epidemic (63%), Dengue virus (62%) ... read more

6,040 Citations



Open accessJournal ArticleDOI: 10.1111/J.1467-9868.2008.00700.X
Abstract: Structured additive regression models are perhaps the most commonly used class of models in statistical applications. It includes, among others, (generalized) linear models, (generalized) additive models, smoothing spline models, state space models, semiparametric regression, spatial and spatiotemporal models, log-Gaussian Cox processes and geostatistical and geoadditive models. We consider approximate Bayesian inference in a popular subset of structured additive regression models, latent Gaussian models, where the latent field is Gaussian, controlled by a few hyperparameters and with non-Gaussian response variables. The posterior marginals are not available in closed form owing to the non-Gaussian response variables. For such models, Markov chain Monte Carlo methods can be implemented, but they are not without problems, in terms of both convergence and computational time. In some practical applications, the extent of these problems is such that Markov chain Monte Carlo sampling is simply not an appropriate tool for routine analysis. We show that, by using an integrated nested Laplace approximation and its simplified version, we can directly compute very accurate approximations to the posterior marginals. The main benefit of these approximations is computational: where Markov chain Monte Carlo algorithms need hours or days to run, our approximations provide more precise estimates in seconds or minutes. Another advantage with our approach is its generality, which makes it possible to perform Bayesian analysis in an automatic, streamlined way, and to compute model comparison criteria and various predictive measures so that models can be compared and the model under study can be challenged.

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Topics: Variable-order Bayesian network (67%), Gibbs sampling (64%), Markov chain Monte Carlo (63%) ... read more

3,369 Citations


Journal ArticleDOI: 10.1007/BF00116466
Julian Besag1, Jeremy York1, Annie Mollié2Institutions (2)
Abstract: There has been much recent interest in Bayesian image analysis, including such topics as removal of blur and noise, detection of object boundaries, classification of textures, and reconstruction of two- or three-dimensional scenes from noisy lower-dimensional views. Perhaps the most straightforward task is that of image restoration, though it is often suggested that this is an area of relatively minor practical importance. The present paper argues the contrary, since many problems in the analysis of spatial data can be interpreted as problems of image restoration. Furthermore, the amounts of data involved allow routine use of computer intensive methods, such as the Gibbs sampler, that are not yet practicable for conventional images. Two examples are given, one in archeology, the other in epidemiology. These are preceded by a partial review of pixel-based Bayesian image analysis.

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Topics: Image restoration (67%), Spatial analysis (51%)

2,903 Citations


Open accessJournal ArticleDOI: 10.1175/JCLI-D-12-00823.1
Suranjana Saha1, Shrinivas Moorthi1, Xingren Wu2, Jiande Wang  +15 moreInstitutions (3)
13 Mar 2014-Journal of Climate
Abstract: The second version of the NCEP Climate Forecast System (CFSv2) was made operational at NCEP in March 2011. This version has upgrades to nearly all aspects of the data assimilation and forecast model components of the system. A coupled reanalysis was made over a 32-yr period (1979–2010), which provided the initial conditions to carry out a comprehensive reforecast over 29 years (1982–2010). This was done to obtain consistent and stable calibrations, as well as skill estimates for the operational subseasonal and seasonal predictions at NCEP with CFSv2. The operational implementation of the full system ensures a continuity of the climate record and provides a valuable up-to-date dataset to study many aspects of predictability on the seasonal and subseasonal scales. Evaluation of the reforecasts show that the CFSv2 increases the length of skillful MJO forecasts from 6 to 17 days (dramatically improving subseasonal forecasts), nearly doubles the skill of seasonal forecasts of 2-m temperatures over the ...

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Topics: Climate Forecast System (61%), Predictability (52%)

1,950 Citations