AUTHOR=Wadford Debra A. , Baumrind Nikki , Baylis Elizabeth F. , Bell John M. , Bouchard Ellen L. , Crumpler Megan , Foote Eric M. , Gilliam Sabrina , Glaser Carol A. , Hacker Jill K. , Ledin Katya , Messenger Sharon L. , Morales Christina , Smith Emily A. , Sevinsky Joel R. , Corbett-Detig Russell B. , DeRisi Joseph , Jacobson Kathleen , the COVIDNet Consortium , Adams Summer , Arunleung Phacharee , Bacinskas Matthew , Baumrind Nikki , Baylis Elizabeth F. , Bernas Cynthia , Bell John M. , Berumen Ricardo , Bouchard Ellen L. , Brown Brandon , Bullick Teal , Chaille Lyndsey , Chen Alice , Cosentino Giorgio , Cruz Yocelyn , D’Angelo Nick , Deldari Mojgan , Espinosa Alex , Espinoza Ambar , Foote Eric M. , Getabecha Shiffen , Gilliam Sabrina , Glaser Carol A. , Glenn Madeleine , Gonzaga Bianca , Gonzales Ydelita , Greengard Melanie , Guevara Hugo , Hacker Jill K. , Hansard Kim , Hatada April , Haw Monica , Huynh Thalia , Jacobson Kathleen , Kath Chantha , Kimsey Paul B. , Ledin Katya , Lemoine Deidra , Lopez Ruth , Messenger Sharon L. , Molinar Blanca , Morales Christina , Munoz Samantha , Nakamura Robert , Osugi Nichole , Padilla Tasha , Pan Chao-Yang , Panditrao Mayuri V. , Preas Chris , Probert Will , Quintana Alexa , Uribe-Fuentes Maria , Ramirez Mayra , Reyes Clarence , Saguar Estela , Salas Maria , Seritan Ioana , Stavig Brandon , Tamnanchit Hilary , Ting Serena , Wadford Debra A. , Wong Cindy , Wright Chelsea , Yagi Shigeo , Servellita Venice , Sotomayor-Gonzalez Alicia , Chiu Charles Y. , Bjork Isabel , Kapp Joshua , van den Bout Anouk , Kephart Ellen , Alnaeeli Mawadda , Poon Hau-Ling , Topper Scott , Shafii Marzieh , Sowko Sara , Trammell Stephanie , Wolfsohn Erik , Ayscue Patrick , Kistler Amy , Crawford Emily , DeRisi Joseph , Tato Cristina , Arboledaz Valeria , Eskin Eleazar , Sathe Laila M. , Skarbinski Jacek , Duque Abigail , Schapiro Jeffrey , Yeung Ivy , Ghatti Rama , Shajani-Yi Zahra , Garrigues Jacob M. , Green Nicole , Hemarajata Peera , Anaya Carlos , Ferguson Donna , Kapuszinsky Beatrix , Ramirez Favian , Sta Agueda Felipe , Crumpler Megan , Wolfe Julia , Corbett-Detig Russell B. , Haussler David , Perry Marc , McBroome Jakob , Duong Nhi , Forester Deborah , Gonzalez Anthony , Victorio Maria J. , Manlutac Anna Liza M. , Corrigan Jeremy , Rhoades Nicholas S. , Castro Lina , Masinde Godfred , Kaur Harmeet , Paniagua-Alexander Monica , Erwin Katrina G. , Miller Glen , Sidhu Frances N. , Jones Morris , Kothari Sangita , Ngo Christopher , Bonin Brandon , Castillo Daniel , Khoshabian Rensen , Andersen Kristian , Zeller Mark , Critchett Lisa , Gonzalez Carlos , Goraichuk Iryna V. , Rees Rachel , Ambrosio Frank , Kapsak Curtis J. , Libuit Kevin G. , Scribner Michelle R. , Sevinsky Joel R. , Smith Emily A. , Wright Sage M. , Cadiz Vanessa B. , Lopez Denise , Rosman Matthew , Bach Bryan , Wyman Stacia , Acharya Charlotte , Davis Ryan , Michelmore Richard , Oakes Melanie , Sandmeyer Suzanne , Borkovich Kathy , Clark Clay H. , Clark Holly , Le Brandon , De Hoff Peter , Jepsen Kristen , Knight Rob , Laurent Louise C. , Aralis Zack , Arias Carolina , Balasanyan Varuzhan , Duhon Mark , Li Xinmin , Chow Eric , Leung Nicole , Martinez Delsy , Miyasaki Tyler T. , Clow Ashlee , Hoffman Jared , Rush Thomas TITLE=Implementation of California COVIDNet – a multi-sector collaboration for statewide SARS-CoV-2 genomic surveillance JOURNAL=Frontiers in Public Health VOLUME=11 YEAR=2023 URL=https://www.frontiersin.org/journals/public-health/articles/10.3389/fpubh.2023.1249614 DOI=10.3389/fpubh.2023.1249614 ISSN=2296-2565 ABSTRACT=Introduction

The SARS-CoV-2 pandemic represented a formidable scientific and technological challenge to public health due to its rapid spread and evolution. To meet these challenges and to characterize the virus over time, the State of California established the California SARS-CoV-2 Whole Genome Sequencing (WGS) Initiative, or “California COVIDNet”. This initiative constituted an unprecedented multi-sector collaborative effort to achieve large-scale genomic surveillance of SARS-CoV-2 across California to monitor the spread of variants within the state, to detect new and emerging variants, and to characterize outbreaks in congregate, workplace, and other settings.

Methods

California COVIDNet consists of 50 laboratory partners that include public health laboratories, private clinical diagnostic laboratories, and academic sequencing facilities as well as expert advisors, scientists, consultants, and contractors. Data management, sample sourcing and processing, and computational infrastructure were major challenges that had to be resolved in the midst of the pandemic chaos in order to conduct SARS-CoV-2 genomic surveillance. Data management, storage, and analytics needs were addressed with both conventional database applications and newer cloud-based data solutions, which also fulfilled computational requirements.

Results

Representative and randomly selected samples were sourced from state-sponsored community testing sites. Since March of 2021, California COVIDNet partners have contributed more than 450,000 SARS-CoV-2 genomes sequenced from remnant samples from both molecular and antigen tests. Combined with genomes from CDC-contracted WGS labs, there are currently nearly 800,000 genomes from all 61 local health jurisdictions (LHJs) in California in the COVIDNet sequence database. More than 5% of all reported positive tests in the state have been sequenced, with similar rates of sequencing across 5 major geographic regions in the state.

Discussion

Implementation of California COVIDNet revealed challenges and limitations in the public health system. These were overcome by engaging in novel partnerships that established a successful genomic surveillance program which provided valuable data to inform the COVID-19 public health response in California. Significantly, California COVIDNet has provided a foundational data framework and computational infrastructure needed to respond to future public health crises.