A Bayesian System to Detect and Track Outbreaks of Influenza-Like Illnesses Including Novel Diseases: Algorithm Development and Validation

Abstract

Background The early identification of outbreaks of both known and novel influenza-like illnesses (ILIs) is an important public health problem. Objective This study aimed to describe the design and testing of a tool that detects and tracks outbreaks of both known and novel ILIs, such as the SARS-CoV-2 worldwide pandemic, accurately and early. Methods This paper describes the ILI Tracker algorithm that first models the daily occurrence of a set of known ILIs in hospital emergency departments in a monitored region using findings extracted from patient care reports using natural language processing. We then show how the algorithm can be extended to detect and track the presence of an unmodeled disease that may represent a novel disease outbreak. Results We include results based on modeling diseases like influenza, respiratory syncytial virus, human metapneumovirus, and parainfluenza for 5 emergency departments in Allegheny County, Pennsylvania, from June 1, 2014, to May 31, 2015. We also include the results of detecting the outbreak of an unmodeled disease, which in retrospect was very likely an outbreak of the enterovirus D68 (EV-D68). Conclusions The results reported in this paper provide support that ILI Tracker was able to track well the incidence of 4 modeled influenza-like diseases over a 1-year period, relative to laboratory-confirmed cases, and it was computationally efficient in doing so. The system was also able to detect a likely novel outbreak of EV-D68 early in an outbreak that occurred in Allegheny County in 2014 as well as clinically characterize that outbreak disease accurately.