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- Title
Simultaneous detection of omicron and other SARS-CoV-2 variants by multiplex PCR MassARRAY technology.
- Authors
Wacharapluesadee, Supaporn; Hirunpatrawong, Piyapha; Petcharat, Sininat; Torvorapanit, Pattama; Jitsatja, Anusara; Thippamom, Nattakarn; Ninwattana, Sasiprapa; Phanlop, Chanchanit; Buathong, Rome; Tangwangvivat, Ratanaporn; Klungthong, Chonticha; Chinnawirotpisan, Piyawan; Hunsawong, Taweewun; Suthum, Krairerk; Komolsiri, Suparerk; Jones, Anthony R.; Fernandez, Stefan; Putcharoen, Opass
- 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.
- Subjects
SARS-CoV-2 Omicron variant; NUCLEOTIDE sequencing; SARS-CoV-2; TURNAROUND time; POLYMERASE chain reaction
- Publication
Scientific Reports, 2023, Vol 13, Issue 1, p1
- ISSN
2045-2322
- Publication type
Article
- DOI
10.1038/s41598-023-28715-9