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  • Title: Simultaneous detection of omicron and other SARS-CoV-2 variants by multiplex PCR MassARRAY technology.
    Author: Wacharapluesadee S, Hirunpatrawong P, Petcharat S, Torvorapanit P, Jitsatja A, Thippamom N, Ninwattana S, Phanlop C, Buathong R, Tangwangvivat R, Klungthong C, Chinnawirotpisan P, Hunsawong T, Suthum K, Komolsiri S, Jones AR, Fernandez S, Putcharoen O.
    Journal: Sci Rep; 2023 Feb 06; 13(1):2089. PubMed ID: 36747014.
    Abstract:
    The rapid emergence of SARS-CoV-2 variants with high severity and transmutability adds further urgency for rapid and multiplex molecular testing to identify the variants. A nucleotide matrix-assisted laser-desorption-ionization time-of-flight mass spectrophotometry (MALDI-TOF MS)-based assay was developed (called point mutation array, PMA) to identify four major SARS-CoV-2 variants of concern (VOCs) including Alpha, Beta, Delta, and Omicron (namely PMA-ABDO) and differentiate Omicron subvariant (namely PMA-Omicron). PMA-ABDO and PMA-Omicron consist of 24 and 28 mutation sites of the spike gene. Both PMA panels specifically identified VOCs with as low as 10 viral copies/µl. The panel has shown a 100% concordant with the Next Generation Sequencing (NGS) results testing on 256 clinical specimens with real-time PCR cycle threshold (Ct) values less than 26. It showed a higher sensitivity over NGS; 25/28 samples were positive by PMA but not NGS in the clinical samples with PCR Ct higher than 26. Due to the mass of nucleotide used to differentiate between wild-type and mutation strains, the co-infection or recombination of multiple variants can be determined by the PMA method. This method is flexible in adding a new primer set to identify a new emerging mutation site among the current circulating VOCs and the turnaround time is less than 8 h. However, the spike gene sequencing or NGS retains the advantage of detecting newly emerged variants.
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