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DIRECT RT-qPCR DETECTION OF SARS-CoV-2 RNA FROM PATIENT NASOPHARYNGEAL SWABS WITHOUT AN RNA EXTRACTION STEP

By Emily A Bruce, Meei-Li Huang, Garrett A. Perchetti, Scott Tighe, Pheobe Laaguiby, Jessica J Hoffman, Diana L Gerrard, Arun K. Nalla, Yulun Wei, Alexander Greninger, Sean A Diehl, David J. Shirley, Debra G. B. Leonard, Christopher Dwight Huston, Beth D. Kirkpatrick, Julie A Dragon, Jessica Crothers, Keith R Jerome, Jason W. Botten

Posted 21 Mar 2020
bioRxiv DOI: 10.1101/2020.03.20.001008 (published DOI: 10.1371/journal.pbio.3000896)

The ongoing COVID-19 pandemic has caused an unprecedented need for rapid diagnostic testing. The Centers for Disease Control and Prevention (CDC) and the World Health Organization (WHO) recommend a standard assay that includes an RNA extraction step from a nasopharyngeal (NP) swab followed by reverse transcription-quantitative polymerase chain reaction (RT-qPCR) to detect the purified SARS-CoV-2 RNA. The current global shortage of RNA extraction kits has caused a severe bottleneck to COVID-19 testing. We hypothesized that SARS-CoV-2 RNA could be detected from NP samples via a direct RT-qPCR assay that omits the RNA extraction step altogether, and tested this hypothesis on a series of blinded clinical samples. The direct RT-qPCR approach correctly identified 92% of NP samples (n = 155) demonstrated to be positive for SARS-CoV-2 RNA by traditional clinical diagnostic RT-qPCR that included an RNA extraction. Thus, direct RT-qPCR could be a front-line approach to identify the substantial majority of COVID-19 patients, reserving a repeat test with RNA extraction for those individuals with high suspicion of infection but an initial negative result. This strategy would drastically ease supply chokepoints of COVID-19 testing and should be applicable throughout the world.

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