Fast SARS-CoV-2 detection by RT-qPCR in preheated nasopharyngeal swab samples

Abstract

Objectives: The gold-standard COVID-19 diagnosis relies on detecting SARS-CoV-2 using RNA purification and one-step retrotranscription and quantitative PCR (RT-qPCR). Based on the urgent need for high-throughput screening, we tested the performance of three alternative, simple and affordable protocols to rapidly detect SARS-CoV-2, bypassing the long and tedious RNA extraction step and reducing the time to viral detection.

Methods: We evaluated three methods based on direct nasopharyngeal swab viral transmission medium (VTM) heating before the RT-qPCR: a) direct without additives; b) in a formamide-EDTA (FAE) buffer, c) in a RNAsnap^TM buffer.

Results: Although with a delay in cycle threshold compared to the gold-standard, we found consistent results in nasopharyngeal swab samples that were subject to a direct 70°C incubation for 10 min.

Conclusions: Our findings provide valuable options to overcome any supply chain issue and help to increase the throughput of diagnostic tests, thereby complementing standard diagnosis.

Keywords: COVID-19; RNA extraction; SARS-CoV-2; diagnosis; fast protocols; sample treatment.

Fig. 1

Schematic diagram of the standard RNA extraction-based protocol (a) compared to the alternative fast protocol (b) and the timesaving estimates for RT-qPCR-based SARS-CoV-2 testing. Indicated times should be taken as conservative estimates as they will be dependent on the personnel skills and the number of samples being assessed on the experiment. Ct, cycle threshold.