•SARS-COV-2 Variant PCR based on the protocol by Vogels et al provides fast results, demands relatively few human and data resources, and delivers high throughput.•In 1,642 SARS-CoV-2 positive samples, no Variant of Concern was missed by Variant PCR, confirmed by whole genome sequencing.•All samples identified as “non-VoC lineages” by the Variant PCR, were confirmed by whole genome sequencing.•The Variant PCR based on the protocol by Vogels et al., is a good and effective method for rapid screening for variants of concern, applicable for most diagnostic high-volume laboratories. The emerging SARS-CoV-2 variants of concern (VoC), B.1.1.7, B.1.351 and P.1, with increased transmission and/or immune evasion, emphasise the need for broad and rapid variant monitoring. Our high-volume laboratory introduced a PCR variant assay (Variant PCR) in January 2021 based on the protocol by Vogels et al. To assess whether Variant PCR could be used for rapid B.1.1.7, B.1.351 and P.1 screening, all positive SARS-CoV-2 airway samples were prospectively tested in parallel using both the Variant PCR and whole genome sequencing (WGS). In total 1,642 SARS-CoV-2 positive samples from individual patients were tested within a time span of 4 weeks. For all samples with valid results from both Variant PCR and WGS, no VoC was missed by Variant PCR (totalling 399 VoC detected). Conversely, all of the samples identified as “other lineages” (i.e., “non-VoC lineages”) by the Variant PCR, were confirmed by WGS. The Variant PCR based on the protocol by Vogels et al., is an effective method for rapid screening for VoC, applicable for most diagnostic laboratories within a pandemic setting. WGS is still required to confirm the identity of certain variants and for continuous surveillance of emerging VoC.