Detection of the Omicron SARS-CoV-2 Lineage and Its BA.1 Variant with Multiplex RT-qPCR

Whole genome sequencing (WGS) is considered the best instrument to track both virus evolution and the spread of new, emerging variants. However, WGS still does not allow the analysis of as many samples as qPCR does. Epidemiological and clinical research needs to develop advanced qPCR methods to identify emerging variants of SARS-CoV-2 while collecting data on their spreading in a faster and cheaper way, which is critical for introducing public health measures. This study aimed at designing a one-step RT-qPCR assay for multiplex detection of the Omicron lineage and providing additional data on its subvariants in clinical samples. The RT-qPCR assay demonstrated high sensitivity and specificity on multiple SARS-CoV-2 variants and was cross-validated by WGS.

Automated summary

Whole genome sequencing is the best tool to track virus evolution and variant spread, but its ability to analyze a large number of samples is still inferior to qPCR. Advanced qPCR methods are needed for epidemiological and clinical research to quickly and affordably identify emerging variants and collect data on their spread. This study designed a one-step RT-qPCR assay for multiplex detection of the Omicron lineage, which showed high sensitivity and specificity and was cross-validated by WGS.