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Epidemiology
Protocol
The Seattle Flu Study: a multiarm community-based prospective study protocol for assessing influenza prevalence, transmission and genomic epidemiology
  1. Helen Y Chu1,
  2. Michael Boeckh2,
  3. Janet A Englund3,
  4. Michael Famulare4,
  5. Barry Lutz5,
  6. Deborah A Nickerson6,7,
  7. Mark Rieder7,
  8. Lea M Starita6,7,
  9. Amanda Adler8,
  10. Elisabeth Brandstetter1,
  11. Chris D Frazer1,
  12. Peter D Han7,
  13. Reena K Gulati9,
  14. James Hadfield1,
  15. Michael Jackson10,
  16. Anahita Kiavand1,
  17. Louise E Kimball2,
  18. Kirsten Lacombe8,
  19. Kira Newman1,
  20. Thomas R Sibley2,
  21. Jennifer K Logue11,
  22. Victoria Rachel Lyon12,
  23. Caitlin R Wolf1,
  24. Monica Zigman Suchsland13,
  25. Jay Shendure6,14,
  26. Trevor Bedford2,6
  1. 1Department of Medicine, University of Washington, Seattle, Washington, USA
  2. 2Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, USA
  3. 3Division of Pediatric Infectious Diseases, Allergy, and Rheumatology, University of Washington, Seattle, Washington, USA
  4. 4Institute for Disease Modeling, Bellevue, Washington, USA
  5. 5Bioengineering, University of Washington, Seattle, Washington, USA
  6. 6Genome Sciences, University of Washington, Seattle, Washington, USA
  7. 7Brotman Baty Institute, University of Washington, Seattle, Washington, USA
  8. 8Seattle Children's Research Institute, Seattle, Washington, USA
  9. 9Centers for Disease Control and Prevention, Atlanta, Georgia, USA
  10. 10Kaiser Permanente, Oakland, California, USA
  11. 11Medicine, University of Washington, Seattle, Washington, USA
  12. 12Family Medicine, University of Washington, Seattle, Washington, USA
  13. 13University of Washington, Seattle, Washington, USA
  14. 14Howard Hughes Medical Institute, Seattle, Washington, USA
  1. Correspondence to Dr Helen Y Chu; helenchu{at}uw.edu

Abstract

Introduction Influenza epidemics and pandemics cause significant morbidity and mortality. An effective response to a potential pandemic requires the infrastructure to rapidly detect, characterise, and potentially contain new and emerging influenza strains at both an individual and population level. The objective of this study is to use data gathered simultaneously from community and hospital sites to develop a model of how influenza enters and spreads in a population.

Methods and analysis Starting in the 2018–2019 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 modelling platforms are in development to characterise the regional spread of influenza and other respiratory pathogens.

Ethics and dissemination The study was approved by the University of Washington’s Institutional Review Board (STUDY00006181). Results will be disseminated through talks at conferences, peer-reviewed publications and on the study website (www.seattleflu.org).

  • influenza
  • protocol
  • respiratory infection
  • virology
  • surveillance
http://creativecommons.org/licenses/by-nc/4.0/

This is an open access article distributed in accordance with the Creative Commons Attribution Non Commercial (CC BY-NC 4.0) license, which permits others to distribute, remix, adapt, build upon this work non-commercially, and license their derivative works on different terms, provided the original work is properly cited, appropriate credit is given, any changes made indicated, and the use is non-commercial. See: http://creativecommons.org/licenses/by-nc/4.0/.

https://doi.org/10.1136/bmjopen-2020-037295

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    Footnotes

    • Twitter @KiraNewmanMDPhD

    • Contributors HYC, MB, JAE, MF, BL, DAN, MR, LMS, JS and TB designed and implemented the protocol. They also wrote, reviewed and edited the written protocol. EB, JL, KN and CW contributed to the design of the prospective clinical and cross-sectional community study arms and also wrote, reviewed and edited the written protocol. RKG, LEK, MJ assisted in the design of the overall protocol. AA and KL contributed to the design of the prospective childcare cohort and reviewed and edited the written protocol. TRS, JH, PDH, CDF and AK contributed to the development of the laboratory and data processing aspects of the protocol and reviewed and edited the written protocol, MZS and VRL contributed to the clinical data aspect of the protocol and reviewed and edited the written protocol.

    • Funding The Seattle Flu Study is funded by Gates Ventures. The funder was not involved in the design of the study, does not have any ownership over the management and conduct of the study, the data, or the rights to publish. Award/Grant number is not applicable.

    • Competing interests HYC receives research support from Sanofi, Cepheid and Genentech/Roche and is a consultant for Merck. JAE receives research support to her institution from AstraZeneca, GlaxoSmithKline, Merck and Novavax and is a consultant for Sanofi Pasteur and Meissa Vaccines.

    • Patient and public involvement Patients and/or the public were not involved in the design, or conduct, or reporting, or dissemination plans of this research.

    • Patient consent for publication Not required.

    • Provenance and peer review Not commissioned; externally peer reviewed.