Evaluation of a fully automated high-throughput SARS-CoV-2 multiplex qPCR assay with built-in screening functionality for del-HV69/70- and N501Y variants such as B.1.1.7

•Pre-screening for relevant SARS-CoV-2 lineages like B.1.1.7 and B.1.351 is possible with PCR-based methods by detecting hallmark mutations.•Multiplex RT-PCR assay for simultaneous detection of Spike-gene Del-69/70 and N501Y.•Fully automated high-throughput setup using the cobas 6800/8800 systems.