NU50CK000630

Northwest Pathogen Genomics Center of Excellence (PGCOE) - The Washington State Department of Health (WA DOH) seeks to be a national leader in the production and use of pathogen genomics, including whole genome sequencing (WGS) data for public health action. We propose to partner with three academic institutions and a local health department to increase the translation of pathogen genomic technologies and innovations in WA and our region.

Through this grant, we will build upon our experience and partnership by establishing a network of these agencies and institutions to accelerate the application of genomics and related technologies in public health. This application is only for the mandatory components (core, response implementation). Coordination of agencies and institutions working at the forefront of genomic epidemiology in research and practice is essential to adequately prepare for infectious disease threats.

Establishing a PGCOE in Washington State will capitalize on our expertise and partnerships in the 5 broad topic areas:

Wet Laboratory Methods:
- Over a decade of experience implementing next-generation sequencing methods at WA PHL
- Partnered with University of Washington (UW) Virology and Northwest Genomics to increase sequencing capacity for SARS-CoV-2
- Partnered with Washington Animal Disease Diagnostic Laboratory (WADDL) to increase availability of notifiable conditions testing across the state

Bioinformatics Technologies and Applications:
- WAPHL has 4 years of experience as the Western Region Bioinformatics Training Lead and regional resource for CDC's Advanced Molecular Detection
- UW Virology has significant bioinformatics capacity coupled with its genomic abilities, including a history of hosting training courses on pathogen genomics data science and visualization

Data Science and Visualization:
- WA DOH epidemiologists and data scientists specializing in data integration, linkage, standardization, visualization, and quality assurance

Genomic Surveillance and Response:
- Genomic epidemiology expertise developed during the SARS-CoV-2 pandemic, housed within the Molecular Epidemiology Program and coordinated with the Bedford Laboratory using a standing IRB exempt determination and data sharing agreement

Field Applications and Investigations:
- A long history of internal coordination between communicable disease epidemiology and the public health laboratories (PHL), as well as with Public Health Seattle & King County (PHSKC), which brings local investigation expertise
- During the SARS-CoV-2 pandemic, WA DOH successfully stood up sequencing capacity at WA PHL and partner laboratories, developed data integration through standardized mechanisms, a weekly surveillance report, a data visualization tool, and multiple analysis projects. We seek to extend this work to other pathogens of public health concern and to other jurisdictions by:
- Developing a networked approach by establishing contracts with academic and public health partners
- Partnering with UW to develop a pathogen agnostic platform
- Ensuring capacity for sequencing efforts through partnership with surge laboratories
- Conducting landscape analyses and developing a roadmap of gaps and opportunities in the use of genomic epidemiology
- Implementing Nextstrain builds and working with the Bedford Laboratory to design and develop additional pipelines
- Partnering within our region and with other PGCOEs to share roadmaps for capacity building, data management processes, and lessons learned around data standardization, data integration, and data linkage

In the short term, we expect to improve our understanding of the current state of genomic epidemiology in public health, increase our use of laboratory and bioinformatics tools, increase capacity to sequence and analyze linked genomic data, and establish systems for data sharing and reporting. In the longer term, we expect greater use of genomic technologies, increased workforce capacity, and greater alignment of US and global genomic epidemiology efforts.

Washington State Department Of Health

NOT APPLICABLE

93.283 - Centers for Disease Control and Prevention Investigations and Technical Assistance

CDC Office of Financial Resources (OFR) [HHS - CDC]

National Center for Emerging and Zoonotic Infectious Diseases (NCEZID) [HHS - CDC]

Washington United States

State-Wide

US Public Health Pathogens Genomics Centers of Excellence (CDC-RFA-CK22-2204)

COVID-19 $7,200,000 (43%) percent of this Cooperative Agreement was funded by COVID-19 emergency acts including the American Rescue Plan Act of 2021.
Amendment Since initial award the total obligations have increased 360% from $3,600,000 to $16,571,235.