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; Christina Lo Porto; Beate Schmitt; Seiwert Nastasja; Abdulrahman Salhab; Sigrun Smola; Jörn Walter

doi:10.1093/ofid/ofab364

Rapid Base-Specific Calling of SARS-CoV-2 Variants of Concern Using Combined RT-PCR Melting Curve Screening and SIRPH Technology

Open Forum Infect Dis. 2021 Jul 14;8(8):ofab364. doi: 10.1093/ofid/ofab364. eCollection 2021 Aug.

Affiliations

¹ Department of Genetics, Saarland University, Saarbrücken, Saarland, Germany.
² Institute of Virology, Saarland University Medical Center, Homburg, Saarland, Germany.

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.

Keywords: SARS-CoV-2; SIRPH; SNuPE; mutation screening; variants of concern.