Fast and cost-effective screening for SARS-CoV-2 variants in a routine diagnostic setting

OBJECTIVE: The aim is to recommend a fast and cost-effective screening procedure for UK/SA SARS-CoV-2 variants in a routing diagnostic setting. METHODS: A rapid procedure using qPCR is described to provide clinicians with information about the two currently most prevalent variants (B1.1.7 and B1.351) that harbour receptor binding domain mutation N501Y. The N501Y specific assay only delivers an amplification signal if the Y501 variant is present. RESULTS: 436 samples initially screened positive for SARS-CoV-2 were randomly selected. Only one of these samples showed a fluorescence signal increase indicative for the Y501 variant. The remaining 435 samples had a melting peak at 54 °C indicating the N501 wildtype. SIGNIFICANCE: The screening of a broad population base can still be performed with the established test system. In case of a positive test for SARS-CoV-2 and corresponding clinical and anamnestic indications, a second qPCR for the mutation N501Y can follow and deliver the result to public health authorities and to the treating physician within a few hours.