Rapid and simultaneous identification of three mutations by the Novaplex™ SARS-CoV-2 variants I assay kit

•Important mutations in nasal swab samples simultaneously detected.•Easy to use and cost-effective PCR-based kit was used for identifying the mutations.•Whole-genome sequencing and mapping to reference genome revealed a novel variant.•Variant with exclusive E484K substitution identified in two samples.•Turnaround time of the kit-based assay was only 2 h. . The emergence of SARS-CoV-2 variants has caused an unexpected rebound globally. The World Health Organization has listed three variants (B.1.1.7, B.1.351, and P.1) as variants of concern. To understand the epidemiology and thereby plan appropriate safety measures, differential identification of the variants is indeed critical. . Although whole-genome sequencing is the gold standard for variant identification, it is time-consuming and relatively expensive. Therefore, a rapid, easy, and cost-effective platform targeting multiple regions of the genome is required. Here, we assessed the usefulness of the Novaplex™ SARS-CoV-2 Variants I Assay kit in identifying mutations in the variants. . We retrospectively examined 30 stored nasal swabs from COVID-19-positive patients tested between November 2020 and March 2021. RNA extracted from these swabs was subjected to the commercial kit and real-time reverse transcription-PCR was performed. To determine the genome sequences of SARS-CoV-2 in the collected samples and deduce the consensus sequences among the identified variants, genome sequencing libraries were prepared and mapped to the reference genome. . Four of the tested samples were determined as variants. Of them, two harbored both H69/V70 deletion and N501Y substitution, whereas two harbored E484K substitution alone. . The variant with E484K substitution alone (“R.1”) has been now categorized as a variant of interest in Japan. Additionally, the kit-based assay was found to be feasible, convenient, and user-friendly in identifying the abovementioned mutations with a turnaround time of only 2 h.