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Comparison of Severe Acute Respiratory Syndrome Coronavirus 2 Screening Using Reverse Transcriptase–Quantitative Polymerase Chain Reaction or CRISPR-Based Assays in Asymptomatic College Students

Educational Objective
To identify the key insights or developments described in this article
1 Credit CME
Key Points

Question  Are CRISPR-based methods a reliable and accessible option to capture severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) outbreaks in a college population?

Findings  In this cohort study, 1808 asymptomatic college students were screened for SARS-CoV-2 status using reverse transcriptase–quantitative polymerase chain reaction (RT-qPCR) and CRISPR-based assays. Nine samples positive for SARS-CoV-2 were detected by RT-qPCR, and 8 were confirmed by CRISPR-based assay and clinical laboratory diagnostic testing, uncovering a change in viral prevalence that coincided with the relaxation of lockdown measures and the rise of coronavirus disease 2019 cases in the community.

Meaning  CRISPR-based methods appear to offer reliable SARS-CoV-2 testing for virus screening and allow capture of the leading edge of an outbreak.

Abstract

Importance  The reopening of colleges and universities in the US during the coronavirus disease 2019 (COVID-19) pandemic is a significant public health challenge. The development of accessible and practical approaches for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) detection in the college population is paramount for deploying recurrent surveillance testing as an essential strategy for virus detection, containment, and mitigation.

Objective  To determine the prevalence of SARS-CoV-2 in asymptomatic participants in a university community by using CREST (Cas13-based, rugged, equitable, scalable testing), a CRISPR-based test developed for accessible and large-scale viral screening.

Design, Setting, and Participants  For this cohort study, a total of 1808 asymptomatic participants were screened for SARS-CoV-2 using a CRISPR-based assay and a point-of-reference reverse transcriptase–quantitative polymerase chain reaction (RT-qPCR) test. Viral prevalence in self-collected oropharyngeal swab samples collected from May 28 to June 11, 2020, and from June 23 to July 2, 2020, was evaluated.

Exposures  Testing for SARS-CoV-2.

Main Outcomes and Measures  SARS-CoV-2 status, viral load, and demographic information of the study participants were collected.

Results  Among the 1808 participants (mean [SD] age, 27.3 [11.0] years; 955 [52.8%] female), 732 underwent testing from May to early June (mean [SD] age, 28.4 [11.7] years; 392 [53.6%] female). All test results in this cohort were negative. In contrast, 1076 participants underwent testing from late June to early July (mean [SD] age, 26.6 [10.5] years; 563 [52.3%] female), with 9 positive results by RT-qPCR. Eight of these positive samples were detected by the CRISPR-based assay and confirmed by Clinical Laboratory Improvement Amendments–certified diagnostic testing. The mean (SD) age of the positive cases was 21.7 (3.3) years; all 8 individuals self-identified as students. These metrics showed that a CRISPR-based assay was effective at capturing positive SARS-CoV-2 cases in this student population. Notably, the viral loads detected in these asymptomatic cases resemble those seen in clinical samples, highlighting the potential of covert viral transmission. The shift in viral prevalence coincided with the relaxation of stay-at-home measures.

Conclusions and Relevance  These findings reveal a shift in SARS-CoV-2 prevalence in a young and asymptomatic population and uncover the leading edge of a local outbreak that coincided with rising case counts in the surrounding county and the state of California. The concordance between CRISPR-based and RT-qPCR testing suggests that CRISPR-based assays are reliable and offer alternative options for surveillance testing and detection of SARS-CoV-2 outbreaks, as is required to resume operations in higher-education institutions in the US and abroad.

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CME Disclosure Statement: Unless noted, all individuals in control of content reported no relevant financial relationships. If applicable, all relevant financial relationships have been mitigated.

Article Information

Accepted for Publication: December 19, 2020.

Published: February 11, 2021. doi:10.1001/jamanetworkopen.2020.37129

Open Access: This is an open access article distributed under the terms of the CC-BY License. © 2021 Rauch JN et al. JAMA Network Open.

Corresponding Author: Carolina Arias, PhD, Department of Molecular, Cellular, and Developmental Biology, University of California, Santa Barbara, Life Sciences Building 2107, Santa Barbara, CA 93106 (carolinaarias@uscb.edu).

Author Contributions: Dr Arias had full access to all the data in the study and takes responsibility for the integrity of the data and the accuracy of the data analysis.

Concept and design: Rauch, Valois, Ponce-Rojas, Lach, Comer, Acosta-Alvear, Wilson, Fitzgibbons, Arias.

Acquisition, analysis, or interpretation of data: Rauch, Valois, Ponce-Rojas, Aralis, Lach, Zappa, Audouard, Solley, Vaidya, Costello, Smith, Javanbakht, Malear, Polito, Arn, Kosik, Acosta-Alvear, Wilson, Fitzgibbons, Arias.

Drafting of the manuscript: Rauch, Lach, Audouard, Smith, Malear, Arn, Acosta-Alvear, Wilson, Fitzgibbons, Arias.

Critical revision of the manuscript for important intellectual content: Rauch, Valois, Ponce-Rojas, Aralis, Zappa, Solley, Vaidya, Costello, Javanbakht, Polito, Comer, Kosik, Acosta-Alvear, Wilson, Fitzgibbons, Arias.

Statistical analysis: Rauch, Valois, Arn, Wilson.

Administrative, technical, or material support: Valois, Ponce-Rojas, Aralis, Lach, Zappa, Solley, Vaidya, Costello, Smith, Javanbakht, Polito, Comer, Kosik, Acosta-Alvear, Wilson, Fitzgibbons.

Supervision: Acosta-Alvear, Fitzgibbons, Arias.

Conflict of Interest Disclosures: Dr Kosik reported a patent for UC Case 2020-715 pending and being a coinventor in a provisional patent filed with the University of California, Santa Barbara (UCSB), Office of Technology and Industry Alliances for the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) detection method known as CREST (Cas13-based, rugged, equitable, scalable testing), which is used in this study. Dr Acosta-Alvear reported a patent for UC Case 2020-715 pending and being a coinventor in a provisional patent filed with the UCSB Office of Technology and Industry Alliances for the SARS-CoV-2 detection method known as CREST, which is used in this study, and a patent for PEARL, a method for nucleic acid isolation. Dr Wilson reported a patent for UC Case 2020-715 pending and being a coinventor in a provisional patent filed with the UCSB Office of Technology and Industry Alliances for the SARS-CoV-2 detection method known as CREST, which is used in this study, and a patent for PEARL, a method for nucleic acid isolation. Dr Arias reported a patent for UC Case 2020-715 pending and being a coinventor in a provisional patent filed with the UCSB Office of Technology and Industry Alliances for the SARS-CoV-2 detection method known as CREST, which is used in this study. No other disclosures were reported.

Additional Contributions: We thank the UCSB Office of Research for their generous support. Mary Ferris, MD, and the UCSB Student Health Service personnel helped establish the preanalytical protocols and collect the samples. Laura Isaac, BS, Erin Ross, BS, and Catelynn Kenner, MPH, at Santa Barbara Cottage Hospital, guided the preparation of the institutional review board protocols. None of these contributors were compensated for this work. We thank all the participants in our study. Finally, we thank all essential workers for keeping society running. Without them, this work would have never happened.

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