During the evolution of the SARS-CoV-2 pandemic, new variants of the virus have emerged and spread worldwide. The increased transmissibility and proclivity of some of these variants to cause more serious disease threatens public health responses against the virus, and they are classified as variants of concern (Variants of Concern, VOCs). While Next-Generation-Sequencing (NGS) is the gold standard to identify VOC, it cannot always be rapidly implemented in some settings to provide information as an early warning tool. Duplex quantitative real time RTqPCR assays offer a sensitive and easy-to-use tool to detect, discriminate, and estimate relative proportions of SARS-CoV-2 variants containing VOC-specific signature mutations from variants lacking it, using allelic discrimination probes. We developed seven multiplexed RTqPCR assays that can detect Alpha (B.1.1.7), Beta (B.1.351), Gamma (P.1), Delta (B.1.617.2), Omicron (B.1.1.529), Omicron BA.1 (B.1.1.529.1) and Omicron BA.2 (B.1.1.529.2) VOCs by targeting 21765_21770DelTACATG, 22281_22289DelCTTTACTTG, 28262_28263InsAACA, 22029_22034DelAGTTCA, 28362_28370DelGAGAACGCA, 22121InsGAGCCAGAA, and 21633_21641DelTACCCCCTG deletions/insertions in their genomes, respectively. Alpha, Beta, Delta, Omicron BA.1 and Omicron BA.2 markers are mapped to the S gene (residues 69/70, 241/243, 157/158, 214, and 25/27 respectively), Gamma insertion is located between the end of ORF8 and the beginning of N gene, and Omicron (B.1.1.529) deletion is mapped to the N gene (residues 31/33). The duplex RTqPCR assay targeting 21765-21770DelTACATG mutation affecting residues HV69/70 has been previously used to estimate the relative proportion of Alpha VOC (Carcereny et al., 2021), and is also suitable to estimate the proportions of Omicron BA.4 and BA.5. All duplex RTqPCR assays targeting signature mutations of VOCs may be used as a complementary tool to NGS for rapid variant tracking and surveillance in wastewater-based epidemiology.