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CRISPR-Cas12-based detection of SARS-CoV-2

Our take —

SARS-CoV-2 DETECTR, RT-LAMP/Cas12 has the potential to be an accurate and rapid alternative for COVID-19 testing without requirement of special equipment. However, the limit of detection is lower compared to other assays (CDC qRT-PCR), and is not currently FDA approved. Additional testing with a diverse sample set is required to better understand real-world accuracy.

Study design

Other

Study population and setting

Nasopharyngeal and/or oropharyngeal swabs collected from both healthy donors and either COVID-19 positive patients or patients positive for other coronaviruses, as determined by RT-PCR testing, were evaluated on newly developed SARS-CoV-2 DETECTR, reverse transcription and isothermal amplification using loop-mediated amplification (RT-LAMP) followed by Cas12 detection of predefined coronavirus sequences (RT-LAMP/Cas12 assay). Results were compared against the CDC SARS-CoV-2 qRT-PCR assay.

Summary of Main Findings

Results of SARS-CoV-2 DETECTR, RT-LAMP/ Cas12 assay were evaluated against CDC SARS-CoV-2 qRT-PCR assay. The limit of detection was higher in DETECTR assays compared to the CDC assay (10 copies/ul vs 1 copy/ul). In 11 SARS-CoV-2 PCR positive respiratory samples, 9/11 positively detected SARS-CoV-2 without cross-reactivity and the 2/11 negative swabs were below limit of detection (<10 copies). In a blind test of 60 samples (30 qRT-PCR COVID-19 positive and 30 qRT-PCR COVID-19 negative), DETECTR assay had a positive predictive agreement of 95% and negative predictive agreement of 100% compared to CDC qRT-PCR assay.

Study Strengths

This study compared performance of a newly developed assay against an FDA approved CDC qPCR test using diverse specimens. This technology removes the need for the extra time and equipment required for thermal cycling, which is necessary for PCR-based approaches. Additionally, this technology can be developed and modified rapidly for new pathogens as they emerge.

Limitations

A presumptive positive result is achieved by detection of one of the two viral gene targets (N gene or E gene), but readout is qualitative and interpretation may vary person to person. Only a small subset of samples were tested, and details about the samples (presence/absence of symptoms, time since infection/symptom onset, etc) are not provided limiting the understanding of utility in real-world diagnostic settings.

Value added

SARS-CoV-2 DETECTR, RT-LAMP/Cas12 assay allows for rapid screening with similar sensitivity and specificity as the gold standard qRT-PCR assays. Results are produced rapidly (30-40 minutes), and can be completed without the need of large equipment.

This review was posted on: 18 July 2020