Dataset Information

Tracking and predicting U.S. influenza activity with a real-time surveillance network.

ABSTRACT: Each year in the United States, influenza causes illness in 9.2 to 35.6 million individuals and is responsible for 12,000 to 56,000 deaths. The U.S. Centers for Disease Control and Prevention (CDC) tracks influenza activity through a national surveillance network. These data are only available after a delay of 1 to 2 weeks, and thus influenza epidemiologists and transmission modelers have explored the use of other data sources to produce more timely estimates and predictions of influenza activity. We evaluated whether data collected from a national commercial network of influenza diagnostic machines could produce valid estimates of the current burden and help to predict influenza trends in the United States. Quidel Corporation provided us with de-identified influenza test results transmitted in real-time from a national network of influenza test machines called the Influenza Test System (ITS). We used this ITS dataset to estimate and predict influenza-like illness (ILI) activity in the United States over the 2015-2016 and 2016-2017 influenza seasons. First, we developed linear logistic models on national and regional geographic scales that accurately estimated two CDC influenza metrics: the proportion of influenza test results that are positive and the proportion of physician visits that are ILI-related. We then used our estimated ILI-related proportion of physician visits in transmission models to produce improved predictions of influenza trends in the United States at both the regional and national scale. These findings suggest that ITS can be leveraged to improve "nowcasts" and short-term forecasts of U.S. influenza activity.

SUBMITTER: Leuba SI

PROVIDER: S-EPMC7707518 | biostudies-literature | 2020 Nov

REPOSITORIES: biostudies-literature

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Tracking and predicting U.S. influenza activity with a real-time surveillance network.

Leuba Sequoia I SI Yaesoubi Reza R Antillon Marina M Cohen Ted T Zimmer Christoph C

PLoS computational biology 20201102 11

Each year in the United States, influenza causes illness in 9.2 to 35.6 million individuals and is responsible for 12,000 to 56,000 deaths. The U.S. Centers for Disease Control and Prevention (CDC) tracks influenza activity through a national surveillance network. These data are only available after a delay of 1 to 2 weeks, and thus influenza epidemiologists and transmission modelers have explored the use of other data sources to produce more timely estimates and predictions of influenza activit ...[more]

PMID: 33137088

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Project description:Seasonal influenza results in substantial annual morbidity and mortality in the United States and worldwide. Accurate forecasts of key features of influenza epidemics, such as the timing and severity of the peak incidence in a given season, can inform public health response to outbreaks. As part of ongoing efforts to incorporate data and advanced analytical methods into public health decision-making, the United States Centers for Disease Control and Prevention (CDC) has organized seasonal influenza forecasting challenges since the 2013/2014 season. In the 2017/2018 season, 22 teams participated. A subset of four teams created a research consortium called the FluSight Network in early 2017. During the 2017/2018 season they worked together to produce a collaborative multi-model ensemble that combined 21 separate component models into a single model using a machine learning technique called stacking. This approach creates a weighted average of predictive densities where the weight for each component is determined by maximizing overall ensemble accuracy over past seasons. In the 2017/2018 influenza season, one of the largest seasonal outbreaks in the last 15 years, this multi-model ensemble performed better on average than all individual component models and placed second overall in the CDC challenge. It also outperformed the baseline multi-model ensemble created by the CDC that took a simple average of all models submitted to the forecasting challenge. This project shows that collaborative efforts between research teams to develop ensemble forecasting approaches can bring measurable improvements in forecast accuracy and important reductions in the variability of performance from year to year. Efforts such as this, that emphasize real-time testing and evaluation of forecasting models and facilitate the close collaboration between public health officials and modeling researchers, are essential to improving our understanding of how best to use forecasts to improve public health response to seasonal and emerging epidemic threats.

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Project description:BACKGROUND:In 2015, the Zika virus spread from Brazil throughout the Americas, posing an unprecedented challenge to the public health community. During the epidemic, international public health officials lacked reliable predictions of the outbreak's expected geographic scale and prevalence of cases, and were therefore unable to plan and allocate surveillance resources in a timely and effective manner. METHODS:In this work, we present a dynamic neural network model to predict the geographic spread of outbreaks in real time. The modeling framework is flexible in three main dimensions (i) selection of the chosen risk indicator, i.e., case counts or incidence rate; (ii) risk classification scheme, which defines the high-risk group based on a relative or absolute threshold; and (iii) prediction forecast window (1 up to 12?weeks). The proposed model can be applied dynamically throughout the course of an outbreak to identify the regions expected to be at greatest risk in the future. RESULTS:The model is applied to the recent Zika epidemic in the Americas at a weekly temporal resolution and country spatial resolution, using epidemiological data, passenger air travel volumes, and vector habitat suitability, socioeconomic, and population data for all affected countries and territories in the Americas. The model performance is quantitatively evaluated based on the predictive accuracy of the model. We show that the model can accurately predict the geographic expansion of Zika in the Americas with the overall average accuracy remaining above 85% even for prediction windows of up to 12?weeks. CONCLUSIONS:Sensitivity analysis illustrated the model performance to be robust across a range of features. Critically, the model performed consistently well at various stages throughout the course of the outbreak, indicating its potential value at any time during an epidemic. The predictive capability was superior for shorter forecast windows and geographically isolated locations that are predominantly connected via air travel. The highly flexible nature of the proposed modeling framework enables policy makers to develop and plan vector control programs and case surveillance strategies which can be tailored to a range of objectives and resource constraints.

Dataset Information

Tracking and predicting U.S. influenza activity with a real-time surveillance network.

Publications

Tracking and predicting U.S. influenza activity with a real-time surveillance network.

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