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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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Autores principales: Feldberg, Liron, Zvi, Anat, Yahalom-Ronen, Yfat, Schuster, Ofir
Formato: Online Artículo Texto
Lenguaje:English
Publicado: MDPI 2023
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10525290/
https://www.ncbi.nlm.nih.gov/pubmed/37760814
http://dx.doi.org/10.3390/biomedicines11092373
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author Feldberg, Liron
Zvi, Anat
Yahalom-Ronen, Yfat
Schuster, Ofir
author_facet Feldberg, Liron
Zvi, Anat
Yahalom-Ronen, Yfat
Schuster, Ofir
author_sort Feldberg, Liron
collection PubMed
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.
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spelling pubmed-105252902023-09-28 Discriminative Identification of SARS-CoV-2 Variants Based on Mass-Spectrometry Analysis Feldberg, Liron Zvi, Anat Yahalom-Ronen, Yfat Schuster, Ofir Biomedicines Brief Report 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. MDPI 2023-08-24 /pmc/articles/PMC10525290/ /pubmed/37760814 http://dx.doi.org/10.3390/biomedicines11092373 Text en © 2023 by the authors. https://creativecommons.org/licenses/by/4.0/Licensee MDPI, Basel, Switzerland. This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY) license (https://creativecommons.org/licenses/by/4.0/).
spellingShingle Brief Report
Feldberg, Liron
Zvi, Anat
Yahalom-Ronen, Yfat
Schuster, Ofir
Discriminative Identification of SARS-CoV-2 Variants Based on Mass-Spectrometry Analysis
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 Brief Report
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10525290/
https://www.ncbi.nlm.nih.gov/pubmed/37760814
http://dx.doi.org/10.3390/biomedicines11092373
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