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

ABSTRACT The ongoing SARS-CoV-2 pandemic has caused an unprecedented need for rapid diagnostic screening [1]. The primary assay employed is a reverse transcription quantitative polymerase chain reaction (RT-qPCR) assay that requires the use of an RNA extraction kit [2,3]. In the United States, the Centers for Disease Control and Prevention (CDC) protocol requires the use of the Qiagen QIAamp DSP Viral RNA Mini kit. The current shortage of this RNA extraction kit during this pandemic has resulted in a severe bottleneck in testing capacity. To address this problem, we tested two alternative strategies: the use of alternative RNA extraction kits or a direct RT-qPCR assay that omits an RNA extraction step altogether. We found that the Qiagen RNeasy Mini kit and the Qiagen RNeasy Micro kit could be substituted for the QIAamp Viral RNA Mini kit. Importantly, we report here that the RT-qPCR assay can be performed directly on patient sample material from a nasal swab, without the need for an RNA extraction step of any kind. Collectively, our findings provide viable options to circumvent supply chain issues in COVID-19 testing. Further, the ability to omit the RNA extraction step from RT-qPCR screening protocols would drastically ease supply chokepoints of COVID-19 screening and should be applicable throughout the world. We would note that our findings are preliminary and based on a single pooled nasopharyngeal swab sample from two previously confirmed positive COVID-19 patients. But due to the urgent need for high volume COVID-19 screening, we wanted to make these findings available immediately while we conduct replicate studies using additional patient samples.