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Automated, miniaturized, and scalable screening of healthcare workers, first responders, and students for SARS-CoV-2 in San Diego County
Sydney C Morgan; Stefan Aigner; Catelyn Anderson; Pedro Belda-Ferre; Peter De Hoff; Clarisse A Marotz; Shashank Sathe; Mark Zeller; Noorsher Ahmed; Xaver Audhya; Nathan A Baer; Tom Barber; Bethany Barrick; Lakshmi Batachari; Maryann Betty; Steven M Blue; Brent Brainard; Tyler Buckley; Jamie Case; Anelizze Castro-Martinez; Marisol Chacon; Willi Cheung; LaVonnye Chong; Nicole G Coufal; Evelyn S Crescini; Scott DeGrand; David P Dimmock; J Joelle Donofrio-Odmann; Emily R Eisner; Mehrbod Estaki; Lizbeth Franco Vargas; Michele Freddock; Robert M Gallant; Andrea Galmozzi; Nina J Gao; Sheldon Gilmer; Edyta M Grzelak; Abbas Hakim; Jonathan Hart; Charlotte Hobbs; Greg Humphrey; Nadja Ilkenhans; Marni Jacobs; Christopher A Kahn; Bhavika K Kapadia; Matthew Kim; Sunil Kurian; Alma L Lastrella; Elijah S Lawrence; Kari Lee; Qishan Liang; Hanna Liliom; Valentina Lo Sardo; Robert Logan; Michal Machnicki; Celestine G Magallanes; Clarence K Mah; Denise Malacki; Ryan J Marina; Christopher Marsh; Natasha K Martin; Nathaniel L Matteson; Daniel J Maunder; Kyle McBride; Bryan McDonald; Daniel McDonald; Michelle McGraw; Audra R Meadows; Michelle Meyer; Amber L Morey; Jasmine R Mueller; Toan T Ngo; Julie Nguyen; Viet Nguyen; Laura J Nicholson; Alhakam Nouri; Victoria Nudell; Eugenio Nunez; Kyle O'Neill; R Tyler Ostrander; Priyadarshini Pantham; Samuel S Park; David Picone; Ashley Plascencia; Isaraphorn Pratumchai; Michael Quigley; Michelle Franc Ragsac; Andrew C Richardson; Refugio Robles-Sikisaka; Christopher A Ruiz; Justin Ryan; Lisa Sacco; Sharada Saraf; Phoebe Seaver; Leigh Sewall; Elizabeth W Smoot; Kathleen M Sweeney; Chandana Tekkatte; Rebecca Tsai; Holly Valentine; Shawn Walsh; August Williams; Min Yi Wu; Bing Xia; Brian Yee; Jason Z Zhang; Kristian G Andersen; Lauge Farnaes; Rob Knight; Gene W Yeo; Louise C Laurent.
Affiliation
  • Sydney C Morgan; University of California San Diego
  • Stefan Aigner; University of California San Diego
  • Catelyn Anderson; The Scripps Research Institute
  • Pedro Belda-Ferre; University of California San Diego
  • Peter De Hoff; University of California San Diego
  • Clarisse A Marotz; University of California San Diego
  • Shashank Sathe; University of California San Diego
  • Mark Zeller; The Scripps Research Institute
  • Noorsher Ahmed; University of California San Diego
  • Xaver Audhya; University of California San Diego
  • Nathan A Baer; University of California San Diego
  • Tom Barber; University of California San Diego
  • Bethany Barrick; Scripps Clinic
  • Lakshmi Batachari; University of California San Diego
  • Maryann Betty; University of California San Diego/Rady Children's Hospital San Diego
  • Steven M Blue; University of California San Diego
  • Brent Brainard; San Diego Fire-Rescue Department
  • Tyler Buckley; The Scripps Research Institute
  • Jamie Case; Scripps Clinic
  • Anelizze Castro-Martinez; University of California San Diego
  • Marisol Chacon; University of California San Diego
  • Willi Cheung; University of California San Diego/ San Diego State University
  • LaVonnye Chong; Rady Children's Hospital San Diego
  • Nicole G Coufal; University of California San Diego/ Rady Children's Hospital San Diego/ Rady Children's Institute for Genomic Medicine
  • Evelyn S Crescini; University of California San Diego
  • Scott DeGrand; Rady Children's Hospital San Diego
  • David P Dimmock; Rady Children's Institute for Genomic Medicine
  • J Joelle Donofrio-Odmann; Rady Children's Hospital San Diego / University of California San Diego / San Diego Fire-Rescue Department
  • Emily R Eisner; University of California San Diego
  • Mehrbod Estaki; University of California San Diego
  • Lizbeth Franco Vargas; University of California San Diego
  • Michele Freddock; Rady Children's Institute for Genomic Medicine
  • Robert M Gallant; University of California San Diego / Salk Institute for Biological Studies
  • Andrea Galmozzi; The Scripps Research Institute
  • Nina J Gao; University of California San Diego
  • Sheldon Gilmer; Rady Children's Hospital San Diego
  • Edyta M Grzelak; The Scripps Research Institute
  • Abbas Hakim; University of California San Diego
  • Jonathan Hart; The Scripps Research Institute
  • Charlotte Hobbs; Rady Children's Institute for Genomic Medicine
  • Greg Humphrey; University of California San Diego
  • Nadja Ilkenhans; Salk Institute for Biological Studies/ Ruperto Carola University
  • Marni Jacobs; University of California San Diego
  • Christopher A Kahn; University of California San Diego/ San Diego Fire-Rescue Department
  • Bhavika K Kapadia; University of California San Diego
  • Matthew Kim; University of California San Diego
  • Sunil Kurian; Scripps Clinic
  • Alma L Lastrella; University of California San Diego
  • Elijah S Lawrence; University of California San Diego
  • Kari Lee; University of California San Diego
  • Qishan Liang; University of California San Diego
  • Hanna Liliom; The Scripps Research Institute
  • Valentina Lo Sardo; The Scripps Research Institute
  • Robert Logan; San Diego Fire-Rescue Department
  • Michal Machnicki; University of California San Diego
  • Celestine G Magallanes; University of California San Diego
  • Clarence K Mah; University of California San Diego
  • Denise Malacki; Rady Children's Hospital San Diego
  • Ryan J Marina; University of California San Diego
  • Christopher Marsh; Scripps Clinic
  • Natasha K Martin; University of California San Diego
  • Nathaniel L Matteson; The Scripps Research Institute
  • Daniel J Maunder; University of California San Diego
  • Kyle McBride; Rady Children's Hospital San Diego
  • Bryan McDonald; Salk Institute for Biological Studies
  • Daniel McDonald; University of California San Diego
  • Michelle McGraw; The Scripps Research Institute
  • Audra R Meadows; March of Dimes Foundation
  • Michelle Meyer; Scripps Clinic
  • Amber L Morey; University of California San Diego/ San Diego State University
  • Jasmine R Mueller; University of California San Diego
  • Toan T Ngo; University of California San Diego
  • Julie Nguyen; The Scripps Research Institute
  • Viet Nguyen; The Scripps Research Institute
  • Laura J Nicholson; The Scripps Research Institute/ Scripps Clinic
  • Alhakam Nouri; University of California San Diego
  • Victoria Nudell; The Scripps Research Institute
  • Eugenio Nunez; University of California San Diego
  • Kyle O'Neill; San Diego Fire-Rescue Department
  • R Tyler Ostrander; University of California San Diego
  • Priyadarshini Pantham; University of California San Diego
  • Samuel S Park; University of California San Diego
  • David Picone; San Diego Fire-Rescue Department
  • Ashley Plascencia; University of California San Diego
  • Isaraphorn Pratumchai; The Scripps Research Institute
  • Michael Quigley; Scripps Clinic
  • Michelle Franc Ragsac; University of California San Diego
  • Andrew C Richardson; Rady Children's Hospital San Diego
  • Refugio Robles-Sikisaka; The Scripps Research Institute
  • Christopher A Ruiz; University of California San Diego
  • Justin Ryan; Rady Children's Hospital San Diego
  • Lisa Sacco; Rady Children's Hospital San Diego
  • Sharada Saraf; The Scripps Research Institute
  • Phoebe Seaver; University of California San Diego
  • Leigh Sewall; The Scripps Research Institute
  • Elizabeth W Smoot; University of California San Diego
  • Kathleen M Sweeney; Rady Children's Hospital San Diego
  • Chandana Tekkatte; University of California San Diego
  • Rebecca Tsai; University of California San Diego
  • Holly Valentine; University of California San Diego
  • Shawn Walsh; The Scripps Research Institute
  • August Williams; University of California San Diego
  • Min Yi Wu; University of California San Diego
  • Bing Xia; University of California San Diego
  • Brian Yee; University of California San Diego
  • Jason Z Zhang; University of California San Diego
  • Kristian G Andersen; The Scripps Research Institute
  • Lauge Farnaes; University of California San Diego / Rady Children's Institute of Genomic Medicine
  • Rob Knight; University of California San Diego
  • Gene W Yeo; University of California San Diego
  • Louise C Laurent; University of California San Diego
Preprint in English | medRxiv | ID: ppmedrxiv-21257885
ABSTRACT
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.
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Full text: Available Collection: Preprints Database: medRxiv Type of study: Diagnostic study / Observational study / Prognostic study Language: English Year: 2021 Document type: Preprint
Full text: Available Collection: Preprints Database: medRxiv Type of study: Diagnostic study / Observational study / Prognostic study Language: English Year: 2021 Document type: Preprint
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