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SARS-CoV-2 Screening Using RT-qPCR or CRISPR-Based Assays
Quick Takes
- CRISPR-based assay is as efficient at detecting SARS-CoV-2 infections in asymptomatic participants as the CDC-recommended RT-qPCR, which is considered the gold standard testing method.
- Furthermore, this CRISPR-based method is scalable, enabling high-throughput testing, and it uses laboratory-generated or off-the-shelf commercially available reagents.
- CRISPR-based assays can offer a solution for areas where access to professional laboratories is limited and there is a need for repetitive sampling.
Study Questions:
What is the prevalence of severe acute respiratory syndrome coronavirus 2 (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?
Methods:
The investigators conducted a cohort study and screened a total of 1,808 asymptomatic participants 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. The main outcomes measures were SARS-CoV-2 status and viral load. Correlations between CRISPR-based assay and the RT-qPCR assay were calculated using the Pearson correlation coefficient, assuming data are from a bivariate normal distribution, using the R function cor.test. Percentage of positive rates were fit using a logistic growth model.
Results:
Among the 1,808 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, 1,076 participants underwent testing from late June to early July (mean [SD] age, 26.6 [10.5] years; 563 [52.3%] female), with nine 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 eight 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:
The authors concluded that 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.
Perspective:
This cohort study reports that CRISPR-based assay is as efficient at detecting SARS-CoV-2 infections in asymptomatic participants as the Centers for Disease Control and Prevention (CDC)-recommended RT-qPCR, which is considered the gold standard testing method. Furthermore, this CRISPR-based method is scalable, enabling high-throughput testing, and it uses laboratory-generated or off-the-shelf commercially available reagents, thus eliminating the restriction of limiting supply chains. These data suggest that CRISPR-based assays can offer a solution for areas where access to professional laboratories is limited and situations in which a high volume of repetitive sampling is necessary, such as a university setting, and allow capture of the leading edge of an outbreak.
Clinical Topics: COVID-19 Hub, Prevention
Keywords: Clinical Laboratory Services, Clustered Regularly Interspaced Short Palindromic Repeats, Coronavirus, COVID-19, Primary Prevention, Reverse Transcriptase Polymerase Chain Reaction, RNA-Directed DNA Polymerase, severe acute respiratory syndrome coronavirus 2, Universities, Viral Load
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