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Simultaneous Detection of Omicron and Other SARS-CoV-2 Variants by Multiplex PCR MassARRAY Technology

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 dev...

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Autores principales: 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
Formato: Online Artículo Texto
Lenguaje:English
Publicado: American Journal Experts 2023
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9882655/
https://www.ncbi.nlm.nih.gov/pubmed/36711810
http://dx.doi.org/10.21203/rs.3.rs-2482226/v1
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author 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
author_facet 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
author_sort Wacharapluesadee, Supaporn
collection PubMed
description 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 hours. However, the spike gene sequencing or NGS retains the advantage of detecting newly emerged variants.
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spelling pubmed-98826552023-01-28 Simultaneous Detection of Omicron and Other SARS-CoV-2 Variants by Multiplex PCR MassARRAY Technology 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 Res Sq Article 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 hours. However, the spike gene sequencing or NGS retains the advantage of detecting newly emerged variants. American Journal Experts 2023-01-17 /pmc/articles/PMC9882655/ /pubmed/36711810 http://dx.doi.org/10.21203/rs.3.rs-2482226/v1 Text en https://creativecommons.org/licenses/by/4.0/This work is licensed under a Creative Commons Attribution 4.0 International License (https://creativecommons.org/licenses/by/4.0/) , which allows reusers to distribute, remix, adapt, and build upon the material in any medium or format, so long as attribution is given to the creator. The license allows for commercial use.
spellingShingle Article
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
Simultaneous Detection of Omicron and Other SARS-CoV-2 Variants by Multiplex PCR MassARRAY Technology
title Simultaneous Detection of Omicron and Other SARS-CoV-2 Variants by Multiplex PCR MassARRAY Technology
title_full Simultaneous Detection of Omicron and Other SARS-CoV-2 Variants by Multiplex PCR MassARRAY Technology
title_fullStr Simultaneous Detection of Omicron and Other SARS-CoV-2 Variants by Multiplex PCR MassARRAY Technology
title_full_unstemmed Simultaneous Detection of Omicron and Other SARS-CoV-2 Variants by Multiplex PCR MassARRAY Technology
title_short Simultaneous Detection of Omicron and Other SARS-CoV-2 Variants by Multiplex PCR MassARRAY Technology
title_sort simultaneous detection of omicron and other sars-cov-2 variants by multiplex pcr massarray technology
topic Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9882655/
https://www.ncbi.nlm.nih.gov/pubmed/36711810
http://dx.doi.org/10.21203/rs.3.rs-2482226/v1
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