Simultaneous detection of omicron and other SARS-CoV-2 variants by multiplex PCR MassARRAY technology
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 assa...
| Main Authors: | , , , , , , , , , , , , , , , , , |
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| Format: | Article |
| Language: | English |
| Published: |
Nature Portfolio
2023-02-01
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| Series: | Scientific Reports |
| Online Access: | https://doi.org/10.1038/s41598-023-28715-9 |
| _version_ | 1828035280625467392 |
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| author | Supaporn Wacharapluesadee Piyapha Hirunpatrawong Sininat Petcharat Pattama Torvorapanit Anusara Jitsatja Nattakarn Thippamom Sasiprapa Ninwattana Chanchanit Phanlop Rome Buathong Ratanaporn Tangwangvivat Chonticha Klungthong Piyawan Chinnawirotpisan Taweewun Hunsawong Krairerk Suthum Suparerk Komolsiri Anthony R. Jones Stefan Fernandez Opass Putcharoen |
| author_facet | Supaporn Wacharapluesadee Piyapha Hirunpatrawong Sininat Petcharat Pattama Torvorapanit Anusara Jitsatja Nattakarn Thippamom Sasiprapa Ninwattana Chanchanit Phanlop Rome Buathong Ratanaporn Tangwangvivat Chonticha Klungthong Piyawan Chinnawirotpisan Taweewun Hunsawong Krairerk Suthum Suparerk Komolsiri Anthony R. Jones Stefan Fernandez Opass Putcharoen |
| author_sort | Supaporn Wacharapluesadee |
| collection | DOAJ |
| description | 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. |
| first_indexed | 2024-04-10T15:44:33Z |
| format | Article |
| id | doaj.art-bc5dd41a487943e3bad13fe4943f54c6 |
| institution | Directory Open Access Journal |
| issn | 2045-2322 |
| language | English |
| last_indexed | 2024-04-10T15:44:33Z |
| publishDate | 2023-02-01 |
| publisher | Nature Portfolio |
| record_format | Article |
| series | Scientific Reports |
| spelling | doaj.art-bc5dd41a487943e3bad13fe4943f54c62023-02-12T12:12:21ZengNature PortfolioScientific Reports2045-23222023-02-0113111110.1038/s41598-023-28715-9Simultaneous detection of omicron and other SARS-CoV-2 variants by multiplex PCR MassARRAY technologySupaporn Wacharapluesadee0Piyapha Hirunpatrawong1Sininat Petcharat2Pattama Torvorapanit3Anusara Jitsatja4Nattakarn Thippamom5Sasiprapa Ninwattana6Chanchanit Phanlop7Rome Buathong8Ratanaporn Tangwangvivat9Chonticha Klungthong10Piyawan Chinnawirotpisan11Taweewun Hunsawong12Krairerk Suthum13Suparerk Komolsiri14Anthony R. Jones15Stefan Fernandez16Opass Putcharoen17Thai Red Cross Emerging Infectious Diseases Clinical Center, King Chulalongkorn Memorial HospitalThai Red Cross Emerging Infectious Diseases Clinical Center, King Chulalongkorn Memorial HospitalThai Red Cross Emerging Infectious Diseases Clinical Center, King Chulalongkorn Memorial HospitalThai Red Cross Emerging Infectious Diseases Clinical Center, King Chulalongkorn Memorial HospitalThai Red Cross Emerging Infectious Diseases Clinical Center, King Chulalongkorn Memorial HospitalThai Red Cross Emerging Infectious Diseases Clinical Center, King Chulalongkorn Memorial HospitalThai Red Cross Emerging Infectious Diseases Clinical Center, King Chulalongkorn Memorial HospitalThai Red Cross Emerging Infectious Diseases Clinical Center, King Chulalongkorn Memorial HospitalDivision of International Communicable Disease Control Ports and Quarantine, Department of Diseases Control, Ministry of Public HealthDivision of Communicable Diseases, Department of Diseases Control, Ministry of Public HealthDepartment of Virology, Armed Forces Research Institute of Medical SciencesDepartment of Virology, Armed Forces Research Institute of Medical SciencesDepartment of Virology, Armed Forces Research Institute of Medical SciencesOffice of Disease Prevention and Control, Region 5, Department of Diseases Control, Ministry of Public HealthOffice of Disease Prevention and Control, Region 5, Department of Diseases Control, Ministry of Public HealthDepartment of Virology, Armed Forces Research Institute of Medical SciencesDepartment of Virology, Armed Forces Research Institute of Medical SciencesThai Red Cross Emerging Infectious Diseases Clinical Center, King Chulalongkorn Memorial HospitalAbstract 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.https://doi.org/10.1038/s41598-023-28715-9 |
| spellingShingle | Supaporn Wacharapluesadee Piyapha Hirunpatrawong Sininat Petcharat Pattama Torvorapanit Anusara Jitsatja Nattakarn Thippamom Sasiprapa Ninwattana Chanchanit Phanlop Rome Buathong Ratanaporn Tangwangvivat Chonticha Klungthong Piyawan Chinnawirotpisan Taweewun Hunsawong Krairerk Suthum Suparerk Komolsiri Anthony R. Jones Stefan Fernandez Opass Putcharoen Simultaneous detection of omicron and other SARS-CoV-2 variants by multiplex PCR MassARRAY technology Scientific Reports |
| 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 |
| url | https://doi.org/10.1038/s41598-023-28715-9 |
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