Automated, miniaturized, and scalable screening of healthcare workers, first responders, and students for SARS-CoV-2 in San Diego County

Abstract

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.

SciScore for 10.1101/2021.06.25.21257885: (What is this?)

Please note, not all rigor criteria are appropriate for all manuscripts.

Table 1: Rigor

Ethics	IRB: The UCSD Institutional Review Boards (IRB) provided human subject protection oversight of the SEARCH study (IRB approval #200470). Consent: Potential healthcare worker participants were informed of the study through an organizational all-user email communication as well as a flyer that was sent to Rady and Scripps Health employees and which contained a QR code that allowed them to fill out an electronic consent form and symptom questionnaire prior to arrival at a study site using REDCap (Research Electronic Data Capture) software hosted at RCHSD Field Sample Permit: An NP swab sample was collected from each participant by sampling the posterior nasopharynx through both nares, according to instructions for NP swab collection from the CDC (https://www.cdc.gov/flu/pdf/professionals/flu-specimen-collection-poster.pdf).
Sex as a biological variable	not detected.
Randomization	not detected.
Blinding	not detected.
Power Analysis	not detected.
Cell Line Authentication	Authentication: Following ANM validation and EUA authorization, we validated ANW and AND sample types with clinically- obtained positive and negative cases for SARS-CoV-2, and using the recently-validated ANM sample type as the comparator.

Table 2: Resources

Software and Algorithms
Sentences	Resources
These other institutions included the University of California, San Diego (UCSD), Children’s Primary Care Medical Group, Rady Children’s Specialists of San Diego, and Sharp HealthCare.	Sharp HealthCare suggested: (re3data.org, RRID:SCR_006782)
Potential healthcare worker participants were informed of the study through an organizational all-user email communication as well as a flyer that was sent to Rady and Scripps Health employees and which contained a QR code that allowed them to fill out an electronic consent form and symptom questionnaire prior to arrival at a study site using REDCap (Research Electronic Data Capture) software hosted at RCHSD	REDCap suggested: (REDCap, RRID:SCR_003445)
Translation of the research workflow into the CLIA environment: The research workflow from the SEARCH study was adapted for clinical use by the EXCITE lab, with the goal of repeated screening of large populations as a component of programs developed to safely increase educational and business activities during the COVID-19 pandemic.	CLIA suggested: None
Five major changes to the SEARCH pipeline were implemented by the EXCITE lab to improve patient acceptability, enhance the safety of testing personnel, increase assay throughput, ensure compliance with College of American Pathologists (CAP) and CLIA regulations, and enable reporting of clinical results to patients’ medical records and to the required public health agencies.	SEARCH suggested: (PIE the search, RRID:SCR_005296)
Samples that tested positive through the EXCITE pipeline were re-extracted and re-amplified to confirm the positive result, and then reported to SD County.	EXCITE suggested: None
Statistical analyses including t- tests and Kruskall-Wallis tests were performed in R (version 4.0.3) or Python (version 3.6.11).	Python suggested: (IPython, RRID:SCR_001658)
u (Desktop version 2019.2.5 and Server version 2019.2.0), Excel 2010 (version 2103), Inkscape (version 1.0), and Leaflet (version 0.7.7).	Excel suggested: None Inkscape suggested: (Inkscape, RRID:SCR_014479)

Results from OddPub: Thank you for sharing your code and data.

Results from LimitationRecognizer: An explicit section about the limitations of the techniques employed in this study was not found. We encourage authors to address study limitations.

Results from TrialIdentifier: No clinical trial numbers were referenced.

Results from Barzooka: We did not find any issues relating to the usage of bar graphs.

Results from JetFighter: We did not find any issues relating to colormaps.

Results from rtransparent:

Thank you for including a conflict of interest statement. Authors are encouraged to include this statement when submitting to a journal.
Thank you for including a funding statement. Authors are encouraged to include this statement when submitting to a journal.
No protocol registration statement was detected.

Results from scite Reference Check: We found no unreliable references.

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Automated, miniaturized, and scalable screening of healthcare workers, first responders, and students for SARS-CoV-2 in San Diego County

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Abstract

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Methods and findings

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