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

Despite substantial progress in the estimation of the burden of influenza through large-scale surveillance studies, there is an ongoing need for improved near-real-time monitoring that is coupled to pandemic preparedness. We envision that pandemic control will require the rapid accrual of actionable information from a diversity of sources. For example, rapid genome sequencing of influenza strains throughout a city could feed the creation of actionable maps that identify new and emerging influenza strains their transmission dynamics. With such a system in place, we can more effectively develop and test strategies to rapidly deploy vaccines, antivirals, and non-pharmaceutical interventions to areas with early influenza detection. This combination of rapid detection and deployment of interventions may provide a new paradigm to contain outbreaks.