Scott DeGrand, Robert M Gallant, Xaver Audhya, Victoria Nudell, Ryan J. Marina, Kristian G. Andersen, Evelyn S Crescini, Peter De Hoff, Tom Barber, Laura Nicholson, Gene W. Yeo, Sheldon Gilmer, Tyler Buckley, Toan T Ngo, Lauge Farnaes, Pedro Belda-Ferre, Chandana Tekkatte, Kyle McBride, Justin Ryan, Catelyn Anderson, Audra R Meadows, J Joelle Donofrio-Odmann, Louise C. Laurent, Clarence K Mah, Kari Lee, Nathaniel L. Matteson, Michelle McGraw, Daniel McDonald, Brian A. Yee, Andrew C. Richardson, Lizbeth Franco Vargas, Abbas Hakim, Shawn I. Walsh, Natasha K. Martin, Lakshmi E. Batachari, Phoebe Seaver, Kathleen M Sweeney, Jasmine R. Mueller, Mehrbod Estaki, Min Yi Wu, Bryan McDonald, Michele Freddock, Rebecca Tsai, L.M. Sewall, Samuel S Park, Matthew Kim, Nicole G. Coufal, Holly Valentine, Charlotte A. Hobbs, Emily Eisner, Julie Nguyen, Elijah S. Lawrence, Viet Ha Nguyen, Michal Machnicki, Nadja Ilkenhans, Brent Brainard, LaVonnye Chong, Marni Jacobs, Robert Logan, Jason Z. Zhang, Shashank Sathe, Amber L Morey, Sunil M. Kurian, David Dimmock, Alhakam Nouri, Anelizze Castro-Martínez, Denise Malacki, Christopher A Ruiz, August Williams, Lisa Sacco, Jamie Case, Noorsher Ahmed, Clarisse Marotz, Daniel Maunder, Isaraphorn Pratumchai, Greg Humphrey, Alma L Lastrella, Michelle Meyer, Michelle Franc Ragsac, Valentina Lo Sardo, Christopher L. Marsh, Eugenio Nunez, Edyta M Grzelak, R Tyler Ostrander, Qishan Liang, Bing Xia, Nina J Gao, Rob Knight, Bhavika K Kapadia, Jonathan Hart, Nathan A Baer, Celestine Magallanes, Bethany Barrick, Elizabeth W Smoot, Priyadarshini Pantham, David Picone, Stefan Aigner, Marisol Chacón, Michael M. Quigley, Sharada Saraf, Willi Cheung, Hanna Liliom, Refugio Robles-Sikisaka, Maryann Betty, Christopher A. Kahn, Andrea Galmozzi, Mark Zeller, Ashley Plascencia, Kyle O'Neill, Sydney C. Morgan, and Steven M. Blue
BackgroundSuccessful containment strategies for SARS-CoV-2, the causative virus of the COVID-19 pandemic, have involved widespread population testing that identifies infections early and enables rapid contact tracing. In this study, we developed a rapid and inexpensive RT- qPCR testing pipeline for population-level SARS-CoV-2 detection, and used this pipeline to establish a clinical laboratory dedicated to COVID-19 testing at the University of California San Diego (UCSD) with a processing capacity of 6,000 samples per day and next-day result turnaround times.Methods and findingsUsing this pipeline, we screened 6,786 healthcare workers and first responders, and 21,220 students, faculty, and staff from UCSD. Additionally, we screened 6,031 preschool-grade 12 students and staff from public and private schools across San Diego County that remained fully or partially open for in-person teaching during the pandemic. Between April 17, 2020 and February 5, 2021, participants provided 161,582 nasal swabs that were tested for the presence of SARS-CoV-2. Overall, 752 positive tests were obtained, yielding a test positivity rate of 0.47%. While the presence of symptoms was significantly correlated with higher viral load, most of the COVID-19 positive participants who participated in symptom surveys were asymptomatic at the time of testing. The positivity rate among preschool-grade 12 schools that remained open for in-person teaching was similar to the positivity rate at UCSD and lower than that of San Diego County, with the children in private schools being less likely to test positive than the adults at these schools.ConclusionsMost schools across the United States have been closed for in-person learning for much of the 2020-2021 school year, and their safe reopening is a national priority. However, as there are no vaccines against SARS-CoV-2 currently available to the majority of school-aged children, the traditional strategies of mandatory masking, physical distancing, and repeated viral testing of students and staff remain key components of risk mitigation in these settings. The data presented here suggest that the safety measures and repeated testing actions taken by participating healthcare and educational facilities were effective in preventing outbreaks, and that a similar combination of risk-mitigation strategies and repeated testing may be successfully adopted by other healthcare and educational systems.