The recent emergence of a novel variant of SARS-CoV-2 called lineage B.1.1.7 has sparked global alarm due to evidence of increased transmissibility, mortality, and uncertainty about vaccine efficacy, thus accelerating worldwide efforts to detect and track the variant. Current approaches to detect the B.1.1.7 variant include sequencing and molecular tests that contain a target assay that fails or results in reduced sensitivity towards the B.1.1.7 variant. Since many countries lack a robust genomic surveillance program and the failed target assays detect multiple unrelated variants that contain similar mutations as B.1.1.7, there is an urgent need to develop molecular tests that can accurately and rapidly identify the B.1.1.7 variant. We have developed a room temperature-stable, multiplexed RT-qPCR test that readily differentiates the B.1.1.7 variant from the most common SARS-CoV-2 variants. The test consists of two assays that target either the common SARS-CoV-2 spike gene or the two deletions in the spike gene (ΔH69/ΔV70 and ΔY144) that are present in the B.1.1.7 variant. Moreover, a simple relative comparison of the Ct values of the two assays permits not only identification of the B.1.1.7 variant but also its differentiation from other variants that harbor only the ΔH69/ΔV70 deletion. Each assay is multiplexed with a human RNase P internal control to assess RNA extraction and assay performance. This test can easily be implemented in diagnostic labs to rapidly scale B.1.1.7 surveillance efforts and is particularly useful in countries with high prevalence of variants possessing only the ΔH69/ΔV70 deletion because current strategies using target failure assays incorrectly identify these as putative B.1.1.7 variants.

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