1. Implementation of California COVIDNet – a multi-sector collaboration for statewide SARS-CoV-2 genomic surveillance
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Debra A. Wadford, Nikki Baumrind, Elizabeth F. Baylis, John M. Bell, Ellen L. Bouchard, Megan Crumpler, Eric M. Foote, Sabrina Gilliam, Carol A. Glaser, Jill K. Hacker, Katya Ledin, Sharon L. Messenger, Christina Morales, Emily A. Smith, Joel R. Sevinsky, Russell B. Corbett-Detig, Joseph DeRisi, Kathleen Jacobson, the COVIDNet Consortium, Summer Adams, Phacharee Arunleung, Matthew Bacinskas, Cynthia Bernas, Ricardo Berumen, Brandon Brown, Teal Bullick, Lyndsey Chaille, Alice Chen, Giorgio Cosentino, Yocelyn Cruz, Nick D’Angelo, Mojgan Deldari, Alex Espinosa, Ambar Espinoza, Shiffen Getabecha, Madeleine Glenn, Bianca Gonzaga, Ydelita Gonzales, Melanie Greengard, Hugo Guevara, Kim Hansard, April Hatada, Monica Haw, Thalia Huynh, Chantha Kath, Paul B. Kimsey, Deidra Lemoine, Ruth Lopez, Blanca Molinar, Samantha Munoz, Robert Nakamura, Nichole Osugi, Tasha Padilla, Chao-Yang Pan, Mayuri V. Panditrao, Chris Preas, Will Probert, Alexa Quintana, Maria Uribe-Fuentes, Mayra Ramirez, Clarence Reyes, Estela Saguar, Maria Salas, Ioana Seritan, Brandon Stavig, Hilary Tamnanchit, Serena Ting, Cindy Wong, Chelsea Wright, Shigeo Yagi, Venice Servellita, Alicia Sotomayor-Gonzalez, Charles Y. Chiu, Isabel Bjork, Joshua Kapp, Anouk van den Bout, Ellen Kephart, Mawadda Alnaeeli, Hau-Ling Poon, Scott Topper, Marzieh Shafii, Sara Sowko, Stephanie Trammell, Erik Wolfsohn, Patrick Ayscue, Amy Kistler, Emily Crawford, Cristina Tato, Valeria Arboledaz, Eleazar Eskin, Laila M. Sathe, Jacek Skarbinski, Abigail Duque, Jeffrey Schapiro, Ivy Yeung, Rama Ghatti, Zahra Shajani-Yi, Jacob M. Garrigues, Nicole Green, Peera Hemarajata, Carlos Anaya, Donna Ferguson, Beatrix Kapuszinsky, Favian Ramirez, Felipe Sta Agueda, Julia Wolfe, David Haussler, Marc Perry, Jakob McBroome, Nhi Duong, Deborah Forester, Anthony Gonzalez, Maria J. Victorio, Anna Liza M. Manlutac, Jeremy Corrigan, Nicholas S. Rhoades, Lina Castro, Godfred Masinde, Harmeet Kaur, Monica Paniagua-Alexander, Katrina G. Erwin, Glen Miller, Frances N. Sidhu, Morris Jones, Sangita Kothari, Christopher Ngo, Brandon Bonin, Daniel Castillo, Rensen Khoshabian, Kristian Andersen, Mark Zeller, Lisa Critchett, Carlos Gonzalez, Iryna V. Goraichuk, Rachel Rees, Frank Ambrosio, Curtis J. Kapsak, Kevin G. Libuit, Michelle R. Scribner, Sage M. Wright, Vanessa B. Cadiz, Denise Lopez, Matthew Rosman, Bryan Bach, Stacia Wyman, Charlotte Acharya, Ryan Davis, Richard Michelmore, Melanie Oakes, Suzanne Sandmeyer, Kathy Borkovich, Clay H. Clark, Holly Clark, Brandon Le, Peter De Hoff, Kristen Jepsen, Rob Knight, Louise C. Laurent, Zack Aralis, Carolina Arias, Varuzhan Balasanyan, Mark Duhon, Xinmin Li, Eric Chow, Nicole Leung, Delsy Martinez, Tyler T. Miyasaki, Ashlee Clow, Jared Hoffman, and Thomas Rush
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SARS-CoV-2 ,genomic surveillance ,COVID-19 ,whole genome sequencing ,cloud-based computing ,data management ,Public aspects of medicine ,RA1-1270 - Abstract
IntroductionThe 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.MethodsCalifornia 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.ResultsRepresentative 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.DiscussionImplementation 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.
- Published
- 2023
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