Automated, miniaturized, and scalable screening of healthcare workers, first responders, and students for SARS-CoV-2 in San Diego County
Authors: Morgan Sydney C , Aigner Stefan , Anderson Catelyn , Belda-Ferre Pedro , De Hoff Peter , Marotz Clarisse A , Sathe Shashank , Zeller Mark , Ahmed Noorsher , Audhya Xaver , Baer Nathan A , Barber Tom , Barrick Bethany , Batachari Lakshmi , Betty Maryann , Blue Steven M , Brainard Brent , Buckley Tyler , Case Jamie , Castro-Martinez Anelizze , Chacón Marisol , Cheung Willi , Chong LaVonnye , Coufal Nicole G , Crescini Evelyn S , DeGrand Scott , Dimmock David P , Joelle Donofrio-Odmann J , Eisner Emily R , Estaki Mehrbod , Vargas Lizbeth Franco , Freddock Michele , Gallant Robert M , Galmozzi Andrea , Gao Nina J , Gilmer Sheldon , Grzelak Edyta M , Hakim Abbas , Hart Jonathan , Hobbs Charlotte , Humphrey Greg , Ilkenhans Nadja , Jacobs Marni , Kahn Christopher A , Kapadia Bhavika K , Kim Matthew , Kurian Sunil , Lastrella Alma L , Lawrence Elijah S , Lee Kari , Liang Qishan , Liliom Hanna , Sardo Valentina Lo , Logan Robert , Machnicki Michal , Magallanes Celestine G , Mah Clarence K , Malacki Denise , Marina Ryan J , Marsh Christopher , Martin Natasha K , Matteson Nathaniel L , Maunder Daniel J , McBride Kyle , McDonald Bryan , McDonald Daniel , McGraw Michelle , Meadows Audra R , Meyer Michelle , Morey Amber L , Mueller Jasmine R , Ngo Toan T , Nguyen Julie , Nguyen Viet , Nicholson Laura J , Nouri Alhakam , Nudell Victoria , Nunez Eugenio , O’Neill Kyle , Tyler Ostrander R , Pantham Priyadarshini , Park Samuel S , Picone David , Plascencia Ashley , Pratumchai Isaraphorn , Quigley Michael , Ragsac Michelle Franc , Richardson Andrew C , Robles-Sikisaka Refugio , Ruiz Christopher A , Ryan Justin , Sacco Lisa , Saraf Sharada , Seaver Phoebe , Sewall Leigh , Smoot Elizabeth W , Sweeney Kathleen M , Tekkatte Chandana , Tsai Rebecca , Valentine Holly , Walsh Shawn , Williams August , Wu Min Yi , Xia Bing , Yee Brian , Zhang Jason Z , Andersen Kristian G , Farnaes Lauge , Knight Rob , Yeo Gene W , Laurent Louise C 
Published: June 2021

Background

Successful 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 findings

Using 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.

Conclusions

Most 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.