Rapid Identification of SARS-CoV-2 Omicron BA.5 Spike Mutation F486V in Clinical Specimens Using a High-Resolution Melting-Based Assay
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) Omicron subvariant BA.5 emerged as of February 2022 and replaced the earlier Omicron subvariants BA.1 and BA.2. COVID-19 genomic surveillance should be continued as new variants seem to subsequently appear, including post-BA.5 subvariants....
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MDPI AG
2022-10-01
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| Series: | Viruses |
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| Online Access: | https://www.mdpi.com/1999-4915/14/11/2401 |
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| author | Akira Aoki Hirokazu Adachi Yoko Mori Miyabi Ito Katsuhiko Sato Masayoshi Kinoshita Masahiro Kuriki Kenji Okuda Toru Sakakibara Yoshinori Okamoto Hideto Jinno |
| author_facet | Akira Aoki Hirokazu Adachi Yoko Mori Miyabi Ito Katsuhiko Sato Masayoshi Kinoshita Masahiro Kuriki Kenji Okuda Toru Sakakibara Yoshinori Okamoto Hideto Jinno |
| author_sort | Akira Aoki |
| collection | DOAJ |
| description | Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) Omicron subvariant BA.5 emerged as of February 2022 and replaced the earlier Omicron subvariants BA.1 and BA.2. COVID-19 genomic surveillance should be continued as new variants seem to subsequently appear, including post-BA.5 subvariants. A rapid assay is needed to differentiate between the currently dominant BA.5 variant and other variants. This study successfully developed a high-resolution melting (HRM)-based assay for BA.4/5-characteristic spike mutation F486V detection and demonstrated that our assay could discriminate between BA.1, BA.2, and BA.5 subvariants in clinical specimens. The mutational spectra at two regions (G446/L452 and F486) for the variant-selective HRM analysis was the focus of our assay. The mutational spectra used as the basis to identify each Omicron subvariant were as follows: BA.1 (G446S/L452/F486), BA.2 (G446/L452/F486), and BA.4/5 (G446/L452R/F486V). Upon mutation-coding RNA fragment analysis, the wild-type fragments melting curves were distinct from those of the mutant fragments. Based on the analysis of 120 clinical samples (40 each of subvariants BA.1, BA.2, and BA.5), this method’s sensitivity and specificity were determined to be more than 95% and 100%, respectively. These results clearly demonstrate that this HRM-based assay is a simple screening method for monitoring Omicron subvariant evolution. |
| first_indexed | 2024-03-09T18:34:32Z |
| format | Article |
| id | doaj.art-ae5d800d3c554ccebb600de64e0ad31e |
| institution | Directory Open Access Journal |
| issn | 1999-4915 |
| language | English |
| last_indexed | 2024-03-09T18:34:32Z |
| publishDate | 2022-10-01 |
| publisher | MDPI AG |
| record_format | Article |
| series | Viruses |
| spelling | doaj.art-ae5d800d3c554ccebb600de64e0ad31e2023-11-24T07:16:36ZengMDPI AGViruses1999-49152022-10-011411240110.3390/v14112401Rapid Identification of SARS-CoV-2 Omicron BA.5 Spike Mutation F486V in Clinical Specimens Using a High-Resolution Melting-Based AssayAkira Aoki0Hirokazu Adachi1Yoko Mori2Miyabi Ito3Katsuhiko Sato4Masayoshi Kinoshita5Masahiro Kuriki6Kenji Okuda7Toru Sakakibara8Yoshinori Okamoto9Hideto Jinno10Faculty of Pharmacy, Meijo University, 150 Yagotoyama, Tempaku-ku, Nagoya 468-8503, JapanAichi Prefectural Institute of Public Health, 7-6 Nagare, Tsuji-machi, Kita-ku, Nagoya 462-8576, JapanFaculty of Pharmacy, Meijo University, 150 Yagotoyama, Tempaku-ku, Nagoya 468-8503, JapanAichi Prefectural Institute of Public Health, 7-6 Nagare, Tsuji-machi, Kita-ku, Nagoya 462-8576, JapanAichi Prefectural Institute of Public Health, 7-6 Nagare, Tsuji-machi, Kita-ku, Nagoya 462-8576, JapanAichi Prefectural Institute of Public Health, 7-6 Nagare, Tsuji-machi, Kita-ku, Nagoya 462-8576, JapanAichi Prefectural Institute of Public Health, 7-6 Nagare, Tsuji-machi, Kita-ku, Nagoya 462-8576, JapanAichi Prefectural Institute of Public Health, 7-6 Nagare, Tsuji-machi, Kita-ku, Nagoya 462-8576, JapanAichi Prefectural Institute of Public Health, 7-6 Nagare, Tsuji-machi, Kita-ku, Nagoya 462-8576, JapanFaculty of Pharmacy, Meijo University, 150 Yagotoyama, Tempaku-ku, Nagoya 468-8503, JapanFaculty of Pharmacy, Meijo University, 150 Yagotoyama, Tempaku-ku, Nagoya 468-8503, JapanSevere acute respiratory syndrome coronavirus 2 (SARS-CoV-2) Omicron subvariant BA.5 emerged as of February 2022 and replaced the earlier Omicron subvariants BA.1 and BA.2. COVID-19 genomic surveillance should be continued as new variants seem to subsequently appear, including post-BA.5 subvariants. A rapid assay is needed to differentiate between the currently dominant BA.5 variant and other variants. This study successfully developed a high-resolution melting (HRM)-based assay for BA.4/5-characteristic spike mutation F486V detection and demonstrated that our assay could discriminate between BA.1, BA.2, and BA.5 subvariants in clinical specimens. The mutational spectra at two regions (G446/L452 and F486) for the variant-selective HRM analysis was the focus of our assay. The mutational spectra used as the basis to identify each Omicron subvariant were as follows: BA.1 (G446S/L452/F486), BA.2 (G446/L452/F486), and BA.4/5 (G446/L452R/F486V). Upon mutation-coding RNA fragment analysis, the wild-type fragments melting curves were distinct from those of the mutant fragments. Based on the analysis of 120 clinical samples (40 each of subvariants BA.1, BA.2, and BA.5), this method’s sensitivity and specificity were determined to be more than 95% and 100%, respectively. These results clearly demonstrate that this HRM-based assay is a simple screening method for monitoring Omicron subvariant evolution.https://www.mdpi.com/1999-4915/14/11/2401severe acute respiratory syndrome coronavirus 2high-resolution meltingOmicron subvariantBA.5F486V mutation |
| spellingShingle | Akira Aoki Hirokazu Adachi Yoko Mori Miyabi Ito Katsuhiko Sato Masayoshi Kinoshita Masahiro Kuriki Kenji Okuda Toru Sakakibara Yoshinori Okamoto Hideto Jinno Rapid Identification of SARS-CoV-2 Omicron BA.5 Spike Mutation F486V in Clinical Specimens Using a High-Resolution Melting-Based Assay Viruses severe acute respiratory syndrome coronavirus 2 high-resolution melting Omicron subvariant BA.5 F486V mutation |
| title | Rapid Identification of SARS-CoV-2 Omicron BA.5 Spike Mutation F486V in Clinical Specimens Using a High-Resolution Melting-Based Assay |
| title_full | Rapid Identification of SARS-CoV-2 Omicron BA.5 Spike Mutation F486V in Clinical Specimens Using a High-Resolution Melting-Based Assay |
| title_fullStr | Rapid Identification of SARS-CoV-2 Omicron BA.5 Spike Mutation F486V in Clinical Specimens Using a High-Resolution Melting-Based Assay |
| title_full_unstemmed | Rapid Identification of SARS-CoV-2 Omicron BA.5 Spike Mutation F486V in Clinical Specimens Using a High-Resolution Melting-Based Assay |
| title_short | Rapid Identification of SARS-CoV-2 Omicron BA.5 Spike Mutation F486V in Clinical Specimens Using a High-Resolution Melting-Based Assay |
| title_sort | rapid identification of sars cov 2 omicron ba 5 spike mutation f486v in clinical specimens using a high resolution melting based assay |
| topic | severe acute respiratory syndrome coronavirus 2 high-resolution melting Omicron subvariant BA.5 F486V mutation |
| url | https://www.mdpi.com/1999-4915/14/11/2401 |
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