High-resolution melting analysis to discriminate between the SARS-CoV-2 Omicron variants BA.1 and BA.2
High-resolution melting (HRM) analysis was conducted to discriminate between SARS-CoV-2 Omicron variant BA.1 (B.1.1.529.1) and subvariant BA.2 (B.1.1.529.2). We performed two-step PCR consisting of the first PCR and the second nested PCR to prepare the amplicon for HRM analysis, which detected G339D...
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| Format: | Article |
| Language: | English |
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Elsevier
2022-09-01
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| Series: | Biochemistry and Biophysics Reports |
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| Online Access: | http://www.sciencedirect.com/science/article/pii/S2405580822001066 |
| _version_ | 1828356254281498624 |
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| author | Takuro Koshikawa Hiroshi Miyoshi |
| author_facet | Takuro Koshikawa Hiroshi Miyoshi |
| author_sort | Takuro Koshikawa |
| collection | DOAJ |
| description | High-resolution melting (HRM) analysis was conducted to discriminate between SARS-CoV-2 Omicron variant BA.1 (B.1.1.529.1) and subvariant BA.2 (B.1.1.529.2). We performed two-step PCR consisting of the first PCR and the second nested PCR to prepare the amplicon for HRM analysis, which detected G339D, N440K, G446S and D796Y variations in the SARS-CoV-2 spike protein. The melting temperatures (Tms) of the amplicons from the cDNA of the Omicron variant BA.1 and subvariant BA.2 receptor binding domain (RBD) in spike protein were the same: 75.2 °C (G339D variation) and 73.4 °C (D796Y variation). These Tms were distinct from those of SARS-CoV-2 isolate Wuhan-Hu-1, and were specific to the Omicron variant. In HRM analyses that detected the N440K and G446S variations, the Tms of amplicons from the cDNA of the Omicron variant BA.1 and subvariant BA.2 RBDs were 73.0 °C (N440K and G446S variations) and 73.5 °C (G446S variation). This difference indicates that the SARS-CoV-2 Omicron variants BA.1 and BA.2 can be clearly discriminated. Our study demonstrates the usefulness of HRM analysis after two-step PCR for the discrimination of SARS-CoV-2 variants. |
| first_indexed | 2024-04-14T02:55:48Z |
| format | Article |
| id | doaj.art-70224dab100f4cbf9c927baaca3c3b23 |
| institution | Directory Open Access Journal |
| issn | 2405-5808 |
| language | English |
| last_indexed | 2024-04-14T02:55:48Z |
| publishDate | 2022-09-01 |
| publisher | Elsevier |
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| series | Biochemistry and Biophysics Reports |
| spelling | doaj.art-70224dab100f4cbf9c927baaca3c3b232022-12-22T02:16:07ZengElsevierBiochemistry and Biophysics Reports2405-58082022-09-0131101306High-resolution melting analysis to discriminate between the SARS-CoV-2 Omicron variants BA.1 and BA.2Takuro Koshikawa0Hiroshi Miyoshi1Department of Microbiology, St. Marianna University School of Medicine, 2-16-1 Sugao, Miyamae, Kawasaki, 216-8511, JapanCorresponding author.; Department of Microbiology, St. Marianna University School of Medicine, 2-16-1 Sugao, Miyamae, Kawasaki, 216-8511, JapanHigh-resolution melting (HRM) analysis was conducted to discriminate between SARS-CoV-2 Omicron variant BA.1 (B.1.1.529.1) and subvariant BA.2 (B.1.1.529.2). We performed two-step PCR consisting of the first PCR and the second nested PCR to prepare the amplicon for HRM analysis, which detected G339D, N440K, G446S and D796Y variations in the SARS-CoV-2 spike protein. The melting temperatures (Tms) of the amplicons from the cDNA of the Omicron variant BA.1 and subvariant BA.2 receptor binding domain (RBD) in spike protein were the same: 75.2 °C (G339D variation) and 73.4 °C (D796Y variation). These Tms were distinct from those of SARS-CoV-2 isolate Wuhan-Hu-1, and were specific to the Omicron variant. In HRM analyses that detected the N440K and G446S variations, the Tms of amplicons from the cDNA of the Omicron variant BA.1 and subvariant BA.2 RBDs were 73.0 °C (N440K and G446S variations) and 73.5 °C (G446S variation). This difference indicates that the SARS-CoV-2 Omicron variants BA.1 and BA.2 can be clearly discriminated. Our study demonstrates the usefulness of HRM analysis after two-step PCR for the discrimination of SARS-CoV-2 variants.http://www.sciencedirect.com/science/article/pii/S2405580822001066SARS-CoV-2OmicronRBDHRM analysisSubvariant |
| spellingShingle | Takuro Koshikawa Hiroshi Miyoshi High-resolution melting analysis to discriminate between the SARS-CoV-2 Omicron variants BA.1 and BA.2 Biochemistry and Biophysics Reports SARS-CoV-2 Omicron RBD HRM analysis Subvariant |
| title | High-resolution melting analysis to discriminate between the SARS-CoV-2 Omicron variants BA.1 and BA.2 |
| title_full | High-resolution melting analysis to discriminate between the SARS-CoV-2 Omicron variants BA.1 and BA.2 |
| title_fullStr | High-resolution melting analysis to discriminate between the SARS-CoV-2 Omicron variants BA.1 and BA.2 |
| title_full_unstemmed | High-resolution melting analysis to discriminate between the SARS-CoV-2 Omicron variants BA.1 and BA.2 |
| title_short | High-resolution melting analysis to discriminate between the SARS-CoV-2 Omicron variants BA.1 and BA.2 |
| title_sort | high resolution melting analysis to discriminate between the sars cov 2 omicron variants ba 1 and ba 2 |
| topic | SARS-CoV-2 Omicron RBD HRM analysis Subvariant |
| url | http://www.sciencedirect.com/science/article/pii/S2405580822001066 |
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