Mutation-specific SARS-CoV-2 PCR Screen: Rapid and Accurate Detection of Variants of Concern and the Identification of a Newly Emerging Variant with Spike L452R Mutation

The emergence of more transmissible and/or more virulent SARS-CoV-2 variants of concern (VOCs) has triggered intensive genomic surveillance, which is costly and difficult to sustain operationally over the long-term. To address this problem, we developed a set of four multiplex mutation-specific PCR-based assays with same-day reporting that can detect five VOCs and three variants of interest (VOIs), as defined in the March 2021 guidelines from the United States (US) Centers for Disease Control and Prevention. The screening results were compared to the whole genome sequencing (WGS) and showed 100% concordance for strain typing for B.1.1.7 (25) and P.1 (5) variants using Spike (S) mutations N501Y, E484K and H69_V70del assays. The S L450R assay, designed to detect the B.1.427/429 VOCs, also identified multiple isolates of a newly emerging multiply-mutated B.1.526.1 variant that is now rapidly increasing in the Eastern US. PCR approaches can be easily adopted in clinical laboratories, provide rapid screening methods to allow early detection of newly emergent variants and to efficiently triage cases for full genomic sequencing.