The application of a novel 5-in-1 multiplex reverse transcriptase–polymerase chain reaction assay for rapid detection of SARS-CoV-2 and differentiation between variants of concern

Abstract

To rapid detect for the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and immediately distinguish whether positive samples represent variants of concern (VOCs), we established a novel 5-in-1 VOC assay. This assay could distinguish among five VOCs: Alpha, Beta, Gamma, Delta, and Omicron, in a single reaction tube. The five variants exhibit different single nucleotide polymorphisms (SNPs) in their viral genome, which can be exploited to distinguish them. We selected target SNPs in the spike gene, including N501Y, P681R, K417N, and deletion H69/V70 for the assay. The limit of detection of each gene locus was 80 copies per PCR reaction. We observed a high consistency among the results when comparing the performance of our 5-in-1 VOC assay, whole gene sequencing, and the Roche VirSNiP SARS-CoV-2 test in retrospectively analyzing 150 clinical SARS-CoV-2 variant positive samples. The 5-in-1 VOC assay offers an alternative and rapid high-throughput test for most diagnostic laboratories in a flexible sample-to-result platform. The assay can also be applied in a commercial platform with completion of the SARS-CoV-2 confirmation test and identification of its variant within 2.5 hours.