SARS-CoV-2 multiplex RT-PCR to detect variants of concern (VOCs) in Malaysia, between January to May 2021

•Two multiplex real-time PCR assays for SARS-CoV-2 spike variants were tested.•The assays detect spike HV69/70 deletion, Y144 deletion, E484K, N501Y, and P681H.•The assays have 98.7–100 % sensitivity compared to next-generation sequencing (NGS).•There was a sharp increase in B.1.351 (beta) variant in Malaysia in early 2021.•Up-to-date assays are a rapid, cheaper alternative to NGS for screening for spike variants.