Journal Article

Nowcasting by Bayesian Smoothing: A flexible, generalizable model for real-time epidemic tracking

Johansson, Michael A., Menzies, Nicolas A., McGough, Sarah F., Lipsitch, Marc

2020

Overview

Achieving accurate, real-time estimates of disease activity is challenged by delays in case reporting. \"Nowcast\" approaches attempt to estimate the complete case counts for a given reporting date, using a time series of case reports that is known to be incomplete due to reporting delays. Modeling the reporting delay distribution is a common feature of nowcast approaches. However, many nowcast approaches ignore a crucial feature of infectious disease transmission-that future cases are intrinsically linked to past reported cases-and are optimized to one or two applications, which may limit generalizability. Here, we present a Bayesian approach, NobBS (Nowcasting by Bayesian Smoothing) capable of producing smooth and accurate nowcasts in multiple disease settings. We test NobBS on dengue in Puerto Rico and influenza-like illness (ILI) in the United States to examine performance and robustness across settings exhibiting a range of common reporting delay characteristics (from stable to time-varying), and compare this approach with a published nowcasting software package while investigating the features of each approach that contribute to good or poor performance. We show that introducing a temporal relationship between cases considerably improves performance when the reporting delay distribution is time-varying, and we identify trade-offs in the role of moving windows to accurately capture changes in the delay. We present software implementing this new approach (R package \"NobBS\") for widespread application and provide practical guidance on implementation.

• Publisher: Public Library of Science,Public Library of Science (PLoS)
• Subject: Bayesian analysis / Case reports / Computer programs / Delay / Dengue / Dengue fever / Disease control / Disease transmission / Economic forecasting / Epidemics / Estimates / Health aspects / Illnesses / Infectious diseases / Influenza / Insurance claims / Medicine and Health Sciences / Methods / People and places / Performance enhancement / Physical Sciences / Probability / Public health / Real time / Reporting / Research and Analysis Methods / Sentinel surveillance / Smoothing / Software / Supervision / Survival analysis / Technology application / Vector-borne diseases / Vectors (Biology)