Discriminative Identification of SARS-CoV-2 Variants Based on Mass-Spectrometry Analysis
The spread of SARS-CoV-2 variants of concern (VOCs) is of great importance since genetic changes may increase transmissibility, disease severity and reduce vaccine effectiveness. Moreover, these changes may lead to failure of diagnostic measures. Therefore, variant-specific diagnostic methods are es...
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| Format: | Article |
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MDPI AG
2023-08-01
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| Series: | Biomedicines |
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| Online Access: | https://www.mdpi.com/2227-9059/11/9/2373 |
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| author | Liron Feldberg Anat Zvi Yfat Yahalom-Ronen Ofir Schuster |
| author_facet | Liron Feldberg Anat Zvi Yfat Yahalom-Ronen Ofir Schuster |
| author_sort | Liron Feldberg |
| collection | DOAJ |
| description | The spread of SARS-CoV-2 variants of concern (VOCs) is of great importance since genetic changes may increase transmissibility, disease severity and reduce vaccine effectiveness. Moreover, these changes may lead to failure of diagnostic measures. Therefore, variant-specific diagnostic methods are essential. To date, genetic sequencing is the gold-standard method to discriminate between variants. However, it is time-consuming (taking several days) and expensive. Therefore, the development of rapid diagnostic methods for SARS-CoV-2 in accordance with its genetic modification is of great importance. In this study we introduce a Mass Spectrometry (MS)-based methodology for the diagnosis of SARS-CoV-2 in propagated in cell-culture. This methodology enables the universal identification of SARS-CoV-2, as well as variant-specific discrimination. The universal identification of SARS-CoV-2 is based on conserved markers shared by all variants, while the identification of specific variants relies on variant-specific markers. Determining a specific set of peptides for a given variant consists of a multistep procedure, starting with an in-silico search for variant-specific tryptic peptides, followed by a tryptic digest of a cell-cultured SARS-CoV-2 variant, and identification of these markers by HR-LC-MS/MS analysis. As a proof of concept, this approach was demonstrated for four representative VOCs compared to the wild-type Wuhan reference strain. For each variant, at least two unique markers, derived mainly from the spike (S) and nucleocapsid (N) viral proteins, were identified. This methodology is specific, rapid, easy to perform and inexpensive. Therefore, it can be applied as a diagnostic tool for pathogenic variants. |
| first_indexed | 2024-03-10T23:01:40Z |
| format | Article |
| id | doaj.art-abf64d72a14b4b8dae35e4725127599b |
| institution | Directory Open Access Journal |
| issn | 2227-9059 |
| language | English |
| last_indexed | 2024-03-10T23:01:40Z |
| publishDate | 2023-08-01 |
| publisher | MDPI AG |
| record_format | Article |
| series | Biomedicines |
| spelling | doaj.art-abf64d72a14b4b8dae35e4725127599b2023-11-19T09:40:22ZengMDPI AGBiomedicines2227-90592023-08-01119237310.3390/biomedicines11092373Discriminative Identification of SARS-CoV-2 Variants Based on Mass-Spectrometry AnalysisLiron Feldberg0Anat Zvi1Yfat Yahalom-Ronen2Ofir Schuster3Department of Analytical Chemistry, Israel Institute for Biological Research (IIBR), Ness Ziona 74100, IsraelDepartment of Biochemistry and Molecular Genetics, Israel Institute for Biological Research (IIBR), Ness Ziona 74100, IsraelDepartment of Infectious Diseases, Israel Institute for Biological Research (IIBR), Ness Ziona 74100, IsraelDepartment of Infectious Diseases, Israel Institute for Biological Research (IIBR), Ness Ziona 74100, IsraelThe spread of SARS-CoV-2 variants of concern (VOCs) is of great importance since genetic changes may increase transmissibility, disease severity and reduce vaccine effectiveness. Moreover, these changes may lead to failure of diagnostic measures. Therefore, variant-specific diagnostic methods are essential. To date, genetic sequencing is the gold-standard method to discriminate between variants. However, it is time-consuming (taking several days) and expensive. Therefore, the development of rapid diagnostic methods for SARS-CoV-2 in accordance with its genetic modification is of great importance. In this study we introduce a Mass Spectrometry (MS)-based methodology for the diagnosis of SARS-CoV-2 in propagated in cell-culture. This methodology enables the universal identification of SARS-CoV-2, as well as variant-specific discrimination. The universal identification of SARS-CoV-2 is based on conserved markers shared by all variants, while the identification of specific variants relies on variant-specific markers. Determining a specific set of peptides for a given variant consists of a multistep procedure, starting with an in-silico search for variant-specific tryptic peptides, followed by a tryptic digest of a cell-cultured SARS-CoV-2 variant, and identification of these markers by HR-LC-MS/MS analysis. As a proof of concept, this approach was demonstrated for four representative VOCs compared to the wild-type Wuhan reference strain. For each variant, at least two unique markers, derived mainly from the spike (S) and nucleocapsid (N) viral proteins, were identified. This methodology is specific, rapid, easy to perform and inexpensive. Therefore, it can be applied as a diagnostic tool for pathogenic variants.https://www.mdpi.com/2227-9059/11/9/2373COVID19SARS-CoV-2variants of concerndiagnosismass-spectrometryLC-MS/MS |
| spellingShingle | Liron Feldberg Anat Zvi Yfat Yahalom-Ronen Ofir Schuster Discriminative Identification of SARS-CoV-2 Variants Based on Mass-Spectrometry Analysis Biomedicines COVID19 SARS-CoV-2 variants of concern diagnosis mass-spectrometry LC-MS/MS |
| title | Discriminative Identification of SARS-CoV-2 Variants Based on Mass-Spectrometry Analysis |
| title_full | Discriminative Identification of SARS-CoV-2 Variants Based on Mass-Spectrometry Analysis |
| title_fullStr | Discriminative Identification of SARS-CoV-2 Variants Based on Mass-Spectrometry Analysis |
| title_full_unstemmed | Discriminative Identification of SARS-CoV-2 Variants Based on Mass-Spectrometry Analysis |
| title_short | Discriminative Identification of SARS-CoV-2 Variants Based on Mass-Spectrometry Analysis |
| title_sort | discriminative identification of sars cov 2 variants based on mass spectrometry analysis |
| topic | COVID19 SARS-CoV-2 variants of concern diagnosis mass-spectrometry LC-MS/MS |
| url | https://www.mdpi.com/2227-9059/11/9/2373 |
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