The Seattle Flu Study expanded our understanding of the transmission of upper respiratory viruses that can cause epidemics. The Seattle Flu Study was a collaborative effort in the Seattle and King County region led by The Brotman Baty Institute, UW Medicine, The Fred Hutchinson Cancer Center, and Seattle Children’s.

A mission to detect and interrupt pandemics: The Seattle Flu Study

Funded by Gates Ventures, the Seattle Flu Study was launched in the fall of 2018, with a mission of transforming how epidemic and pandemic outbreaks are detected, monitored, and controlled. In its first year, the Seattle Flu Study created the infrastructure to sample acute respiratory infections in the Seattle region through enhanced clinical and community surveillance, public recruitment programs, and rapid diagnostic tests.

In its second year, the Seattle Flu Study prototyped rapid, early interventions to address types of influenza outside of clinical settings. It also included the collection of community swabs via kiosks placed around the city, hospital residual samples, as well as provided test kits to families, and offered testing in homeless shelters, among other activities.

Prior to COVID-19, the Seattle Flu Study collected and processed more than 19,000 nasal swab samples, sequenced more than 2,300 influenza genomes, and developed and distributed 3,200 self-administered rapid-diagnostic tests to quantify transmission of influenza to the Seattle area.

As the COVID-19 pandemic began in early January 2020, the Seattle Flu Study team pivoted to detect and understand the spread of SARS-CoV-2 throughout the Seattle area. The Seattle Flu Study became one of the first research groups to conduct genome sequencing of the virus, which informed understanding of how COVID-19 was changing and spreading in the King County area. The Seattle Flu Study team analyzed approximately 9,420 SARS-CoV-2 (the virus that causes COVID-19) genomes from March 2020 to July 2022, and trained staff from the Public Health Laboratories of the Washington Department of Health in genomic sequencing of the virus.

Response to COVID-19: the Greater Seattle Coronavirus Assessment Network

The COVID-19 pandemic created an extraordinary need for rapid, reliable, and high-volume testing in the Seattle area. In response, the Greater Seattle Coronavirus Assessment Network (SCAN) was created to scale up detection and sequencing of SARS-CoV-2. SCAN, funded by Gates Ventures, was the first community surveillance program for COVID-19 in the United States.

The SCAN study collected at-home self-administered nasal swabs from people across Seattle and King County who were feeling sick (symptomatic), as well as a small number of people with no symptoms (asymptomatic). By providing at-home delivery and pick up of the nasal kits, individuals were able to perform the test from their homes, thus reducing exposure to the general public.

Using a lab-developed test for SARS-CoV-2 developed by the Seattle Flu Study team, SCAN provided a quarter of all COVID-19 testing in King County in the early months of the pandemic. This supplied critical data to public and state health officials about how the pandemic was spreading. SCAN also conducted crucial outreach and education to the public and provided testing to underserved populations. In total, 69,900 COVID-19 tests were provided from March 2020 to July 2022 in King and Pierce Counties.

Beyond the laboratory, the SCAN team contributed to pandemic response efforts across the state. Partnerships with Public Health − Seattle & King County allowed SCAN’s findings to inform the Washington State Department of Health to expand its genome sequencing capacity with training, joint analyses, and ongoing communication.

In the early days of the pandemic, the SCAN team provided regular situation updates about COVID-19 transmission to the Washington State Department of Health and Public Health − Seattle & King County, sharing real-time findings on how new variants of the virus were affecting the spread of COVID-19 and hospitalization rates. SCAN also supported contact-tracing efforts by offering free testing to close contacts of individuals who tested positive through SCAN, as well as those referred to SCAN from Public Health − Seattle & King County’s contact tracing team.

Insights for the future

The Seattle Flu Study and SCAN studies uncovered key insights into ways to better predict and respond to future outbreaks at the local and national levels. In King County, effective collaboration and protocols were established among public health agencies, the University of Washington, and the private sector. These relationships will be maintained and strengthened in the face of future outbreaks.

At the national level, a new and more flexible regulatory framework is needed to ensure research studies and clinical testing are conducted nimbly and ethically and provide maximum benefit to society. Specifically, this publication in Nature Medicine describes the hurdles the Seattle Flu Study faced from conflicting state and federal regulations in testing for SARS-CoV-2 in the community, and the lessons this experience holds for future pandemic surveillance programs.

The insights from the Seattle Flu Study and SCAN resulted in five key recommendations for a preparedness framework to be considered before another pandemic occurs:

  1. Community surveillance and engagement, and collaboration with public health agencies
  2. Data collection and accurate analysis
  3. Modeling transmission dynamics and genomic epidemiology
  4. Regulatory oversight of clinical laboratory testing under current federal standards
  5. Laboratory flexibility to help address emerging pathogens and supply chain disruptions

Creation of the Seattle Flu Alliance

After four years of contributing to scientific discovery and improving public health in the Seattle region, the Seattle Flu Study and SCAN research studies ended active recruitment on July 31, 2022. Research, data collection, and analyses will continue with the outcomes of these analyses being shared with policy makers and researchers via peer-reviewed journal publications and ongoing collaborations.

Launched in 2022, the Seattle Flu Alliance reflects a new expansion of researchers and initiatives related to respiratory pathogens. The mission of the Seattle Flu Alliance is to understand how respiratory viruses spread and evolve, sharing that knowledge to prevent illness and death.

The Seattle Flu Alliance builds on the insights of the Seattle Flu Study and SCAN to continue research and find solutions to address respiratory viruses that pose a threat to public health. The aims of the Seattle Flu Alliance are to research and understand the times of year that certain respiratory illnesses tend to spread and become a problem; and the risk factors, demographics (such as age, race, and income), and individual actions that influence the spread of these illnesses.


We would like to thank the following partners for their support of SCAN:

  • Washington State Department of Health
  • University of Washington School of Medicine, Department of Virology
  • Tacoma-Pierce County Health Department
  • US Centers for Disease Control and Prevention

We would like to thank Public Health – Seattle & King County for its partnership with SCAN as well as its collaborations with Healthier Here and local community-based organizations to better understand and support access to testing and safety among the most impacted communities in and around King County.

Financial Support

The Seattle Flu Study and SCAN were funded by Gates Ventures, the private office of Bill Gates.

The Seattle Flu Alliance is funded by the University of Washington, the National Institutes of Health, the US Centers for Disease Control and Prevention, Tacoma-Pierce County Health Department, and private philanthropic donors.


Visit our Publications page for scientific papers, media releases, and updates.


For a historical view of dashboards produced for SCAN, please see here.