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

• Prevalence of ARI specifically attributable to influenza, as well as to RSV, adenovirus, coronavirus, rhinovirus and other respiratory pathogens • Clinical, geospatial, and sociodemographic characteristics of participants with ARI respiratory pathogens other than influenza • Geospatial mapping of ARI cases attributable to other respiratory pathogens • Genetic diversity of circulating strains of respiratory pathogens in the Seattle metropolitan area, by age, vaccine status, site of collection, and home census tract • Impact of bacterial co-detection on viral ARI disease severity and outcomes • Molecular epidemiology and transmission dynamics of respiratory pathogens within sites of collection • Impact of viral co-infection on viral ARI disease severity and outcomes • Prevalence and concordance of environmental sampling by sample type and sampling location • Viral kinetics of respiratory pathogens among individuals with longitudinal sample collection • Prevalence and predictors of care-seeking and influenza vaccine receipt within participants • Viral load and its relationship with clinical disease characteristics in both single and multiple virus infections • Correlation of viral load with molecular markers of nasal swab sampling efficiency • Probability of influenza based on individual-level factors, including symptoms Data collection methods For participants enrolled in the clinical cross-sectional or prospective clinical arms, EMR data are obtained through the clinical data warehouse, which consolidates patient-level medical data from multiple sources. Survey data from eligible and enrolled participants in the community cross-sectional and prospective arms are collected through the FluTrack app (Audere, Seattle, WA), a mobile-enabled app created for the Seattle Flu Study and administered on a tablet. For participants unable or unfamiliar with the use of the tablet, questionnaires on the FluTrack app are administered by study staff verbally in English or Spanish. If the participant is under 7 years old, their LAR completes the questionnaire on their behalf. For participants aged 7-12 years, the LAR may decide whether to complete the survey on the participant's behalf or in collaboration. Participants aged 13 years or older complete the questionnaire. Data are collected on US Flu VE Network enrollees via interview and extraction from EMR and administrative healthcare databases.