Accuracy of a RT-qPCR SARS-CoV-2 detection assay without prior RNA extraction

Abstract

The current COVID-19 pandemic constitutes a threat to the population worldwide with over 21 million infected people. There is an urgent need for the development of rapid and massive detection tools as well as the identification and isolation of infected individuals. we sought to evaluate different RT-qPCR kits and protocols to evaluate the best approach to be used omitting an RNA extraction step. We have investigated the sensitivity and performance of different commercially available RT-qPCR kits in detecting SARS-CoV-2 using 80 extracted RNA and NSS from COVID-19 diagnosed patients. We evaluated the ability of each kit to detect viral RNA from both kit-extracted or directly from a pre-boiled NSS observing that direct RNA detection is possible when Ct values are lower than 30 with the three kits tested. Since SARS-CoV-2 testing in most locations occurs once COVID-19 symptoms are evident and, therefore, viral loads are expected to be high, our protocol will be useful in supporting SARS-CoV-2 diagnosis, especially in America where COVID-19 cases have exploded in the recent weeks as well as in low- and middle-income countries, which would not have massive access to kit-based diagnosis. The information provided in this work paves the way for the development of more efficient SARS-CoV-2 detection approaches avoiding an RNA extraction step.

Keywords: 2019-nCoV; COVID-19; RNA extraction; RT-PCR; SARS-CoV-2.

Fig. 1

SARS-CoV-2 RNA can be detected in direct nasopharyngeal swabs with less sensitivity in RNA simples with >30 Ct values. A. RT-qPCR amplification of SARS-CoV-2 RNA (light blue) and direct nasopharyngeal swab samples preserved in PBS (NSS, light red) using Roche, BGI and SunYat-Sen University as commercial diagnosis kits. Statistical analysis was done using a t-test with Welch's correction. Each dot corresponds to individual data points. B. A positive percentage agreement between RNA (reference) and NSS RT-PCR Bars represent the 95 % confidence intervals computed by the hybrid Wilson/Brown method. C. Total positive percentage agreement between RNA (reference) and NSS RT-qPCR results separated as Ct <30 and >30 in RNA amplification. Bars represent the 95 % confidence intervals computed by the hybrid Wilson/Brown method (For interpretation of the references to colour in this figure legend, the reader is referred to the web version of this article).