In vitro evaluation of the effect of mutations in primer binding sites on detection of SARS-CoV-2 by RT-qPCR

•A mismatch in the forward primer has a stronger effect on SARS-CoV-2 RT-PCR than in the reverse primer.•The ambiguities in the Charité RdRP primer set are unnecessary and RT-PCR is more sensitive without them.•The Seegene Allplex kit has a 3 nt mismatch in the N assay for variant B1.1.7, leading to a drop in ct values.