The Seattle Flu Study: a multi-arm community-based prospective study protocol for assessing influenza prevalence, transmission, and genomic epidemiology

Helen Y. Chu; Michael Boeckh; Janet A. Englund; Michael Famulare; Barry R. Lutz; Deborah A Nickerson; Mark J. Rieder; Lea M Starita; Amanda Adler; Elisabeth Brandstetter; Chris D. Frazar; Peter D. Han; Reena K. Gularti; James Hadfield; Michael L. Jackson; Anahita Kiavand; Louise E. Kimball; Kirsten Lacombe; Jennifer Logue; Victoria Lyon; Kira L. Newman; Thomas R. Sibley; Monica L. Zigman Suschsland; Caitlin Wolf; Jay Shendure; Trevor Bedford

Starting in the 2018-19 season, we have been enrolling individuals with acute respiratory illness from community sites throughout the Seattle metropolitan area, including clinics, childcare facilities, Seattle-Tacoma International Airport, workplaces, college campuses, and homeless shelters. At these sites, we collect clinical data and mid-nasal swabs from individuals with at least two acute respiratory symptoms. Additionally, we collect residual nasal swabs and data from individuals who seek care for respiratory symptoms at four regional hospitals. Samples are tested using a multiplex molecular assay, and influenza whole genome sequencing is performed for samples with influenza detected. Geospatial mapping and computational modeling platforms are in development to characterize the regional spread of influenza and other respiratory pathogens.