Rapid Base-Specific Calling of SARS-CoV-2 Variants of Concern Using Combined RT-PCR Melting Curve Screening and SIRPH Technology
Sascha Tierling, Kathrin Kattler, Markus Vogelgesang, Thorsten Pfuhl, Stefan Lohse, C. Lo Porto, B. Schmitt, Nastasja Seiwert, Abdulrahman Salhab, Sigrun Smola, Jörn Walter
Abstract
BACKGROUND: The emergence of novel variants of concern of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) demands fast and reliable detection of such variants in local populations. METHODS: Here we present a cost-efficient and fast workflow combining a prescreening of SARS-CoV-2-positive samples using reverse transcription polymerase chain reaction melting curve analysis with multiplexed IP-RP-HPLC-based single nucleotide primer extensions. RESULTS: The entire workflow from positive SARS-CoV-2 testing to base-specific identification of variants requires about 24 hours. CONCLUSIONS: We applied the sensitive method to monitor local variant of concern outbreaks in SARS-CoV-2-positive samples collected in a confined region of Germany.