Extraction-Free Methods for the Detection of SARS-CoV-2 by Reverse Transcription-PCR: a Comparison with the Cepheid Xpert Xpress SARS-CoV-2 Assay across Two Medical Centers

Reverse transcription-PCR (RT-PCR) is the gold standard for the diagnosis of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection; however, testing has been complicated by supply shortages and long turnaround times. A major limiting factor early in the coronavirus disease 2019 (COVID-19) pandemic was the lack of ready availability of the reagents for RNA extraction, which remains an expensive and time-consuming part of some testing modalities. Of great interest, extraction-free methods for use with both nasopharyngeal and saliva sources have been investigated in pilot studies (1–6). In this study, we assessed the detection of SARS-CoV-2 in two clinical laboratories from 144 nasopharyngeal specimens, utilizing an extraction-free method and RT-PCR using CDC primers/probe (Fig. 1A). We compared this method (Direct N2) with the widely used Cepheid Xpert Xpress SARS-CoV-2 assay, which has FDA emergency use authorization (EUA).