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A novel strategy for the detection of SARS-CoV-2 variants based on multiplex PCR-MALDI-TOF MS

Background The second wave of coronavirus disease 2019 (COVID-19) has been incessantly causing catastrophe worldwide, and the emergence of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants causes further uncertainty regarding epidemic risk. Here, a novel strategy for the detection of SARS-CoV-2 variants using multiplex PCR coupled with MALDI-TOF MS was developed. Methods Plasmids carrying gene sequences containing 9 mutation types in 7 mutated sites (HV6970del, N501Y, K417N, P681H, D614G, E484K, L452R, E484Q and P681R) in the receptor-binding domain of the spike protein of SARS-CoV-2 variants were synthesized. Using the nucleic acid sequence of SARS-CoV-2 nonvariant and a synthetic SARS-CoV-2 variant-carrying plasmid, a MALDI-TOF MS method based on the single-base mass probe extension of multiplex PCR amplification products was established to detect the above nine mutation types. The detection limit of this method was determined via the concentration gradient method. Twenty-one respiratory tract pathogens (9 bacteria, 11 respiratory viruses) and pharyngeal swab nucleic acid samples from healthy people were selected for specific validation. Sixteen samples from COVID-19 patients were used to verify the accuracy of this method. Results The 9 mutation types could be detected simultaneously by triple PCR amplification coupled with MALDI-TOF MS. SARS-CoV-2 and all six variants (B.1.1.7, B.1.351, B.1.429, B.1.526, P.1 and B.1.617) could be identified. The detection limit for all 9 sites was 1560 copies. The specificity of this method was 100%, and the accuracy of real-time PCR CT values less than 30 among positive samples was 100%. This method is open and extensible, and can be used in a high-throughput manner, easily allowing the addition of new mutation sites as needed to identify and track new SARS-CoV-2 variants as they emerge. Conclusions Multiplex PCR-MALDI-TOF MS provides a new detection option with practical application value for SARS-CoV-2 and its variant infection.