A qualitative RT-PCR assay for the specific identification of the SARS-CoV-2 B.1.1.529 (Omicron) Variant of Concern

•A one-step RT-PCR assay for the specific detection of SARS-CoV-2 Omicron.•The assay was evaluated in silico, and validaded on synthetic RNA genomes and clinical samples.•The analytical sensitivity and specificity of the assay allow the fast detection of SARS-CoV-2 Omicron even at low concentration level.•In contrast to other RT-PCR assays based on the deletion 69-70, this assay is able to detect the Omicron lineage BA.1 but also the currently prevalent BA.2 lineage.•The assay represents an advantageous alternative to sequencing or to the S gene target failure assays.