A new strategy of multiplex real-time RT-qPCR assay for differentiating Omicron variants from other SARS-CoV-2 lineages.

The global dissemination of severe acute respiratory syndrome coronavirus type 2 (SARS-CoV-2) Omicron variants has been characterized by a distinct 9-base pair (bp) deletion within the nucleocapsid (N) gene, a genomic feature absent in previously circulating variants. In response to this unique characteristic, we have developed an innovative amplicon-competition strategy to differentiate Omicron lineages from other SARS-CoV-2 variants using a real-time reverse-transcriptase polymerase chain reaction (RT-PCR) assay. This novel methodology demonstrates high specificity and sensitivity, effectively detecting viral loads ranging from 1500 to 1.5x10⁶ copies per milliliter in nasopharyngeal swab specimens. The potential applications of this approach extend beyond current needs, providing a robust framework for the genomic characterization of future variants exhibiting unique genetic signatures. [ABSTRACT FROM AUTHOR]