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

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

We collected data on approximately 53,000 cases of dengue in Puerto Rico and 2.77 million cases of ILI in the United States over a 21-year (1092 weeks) and 3.75-year (196 weeks) period, respectively. Time-stamped weekly dengue data for laboratory-confirmed cases of dengue in Puerto Rico were collected by the Puerto Rico Department of Health and Centers for Disease Control and Prevention. The times used for the analysis were the time of onset as reported by the reporting clinician and the time of laboratory report completion. ILI data originated from the U.S. Outpatient Influenza-like Illness Surveillance Network (ILINet), which consolidates information from over 2000 outpatient healthcare providers in the United States who report to the CDC on the number of patients with ILI. The times used for the analysis were the week of ILI-related care seeking and the week when those cases were posted online in FluView (https://gis.cdc.gov/grasp/fluview/fluportaldashboard.html) as collected in the DELPHI epidemiological data API (https://github.com/cmu-delphi/delphi-epidata). ILI data with delays of more than 6 months occasionally had irregularities, so we restricted the analyses to delays of up to 6 months.