RT-qPCR assay for detection of British (B.1.1.7) and South Africa (B.1.351) variants of SARS-CoV-2

Less than a year following the SARS-CoV-2 outbreak, variants of concern have emerged in the form of the British variant B.1.1.7 and the South Africa variant B.1.351. Due to their high infectivity and morbidity, it is crucial to quickly and effectively detect them. Current methods of detection are either time-consuming, expensive or indirect. Here, we report the development of a rapid, cost-effective and direct RT-qPCR method for detection of the two variants of concern. We developed and validate a detection system for the detection of the B.1.1.7 variant and another single detection set for the B.1.351 variant. The developed approach was characterized and tested on wastewater samples and illustrated that all primers and probes were sensitive and specific. The novel system presented here will allow proper response and pandemic containment with regard to these variants. In addition, it may provide a basis for developing tools for the detection of additional variants of concern.