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How concerning is a SARS-CoV-2 variant of concern? Computational predictions and the variants labeling system

In this study, we evaluated the use of a predictive computational approach for SARS-CoV-2 genetic variations analysis in improving the current variant labeling system. First, we reviewed the basis of the system developed by the World Health Organization (WHO) for the labeling of SARS-CoV-2 genetic v...

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Autores principales: Ashoor, Dana, Marzouq, Maryam, Trabelsi, Khaled, Chlif, Sadok, Abotalib, Nasser, Khalaf, Noureddine Ben, Ramadan, Ahmed R., Fathallah, M-Dahmani
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Frontiers Media S.A. 2022
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9399656/
https://www.ncbi.nlm.nih.gov/pubmed/36034694
http://dx.doi.org/10.3389/fcimb.2022.868205
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author Ashoor, Dana
Marzouq, Maryam
Trabelsi, Khaled
Chlif, Sadok
Abotalib, Nasser
Khalaf, Noureddine Ben
Ramadan, Ahmed R.
Fathallah, M-Dahmani
author_facet Ashoor, Dana
Marzouq, Maryam
Trabelsi, Khaled
Chlif, Sadok
Abotalib, Nasser
Khalaf, Noureddine Ben
Ramadan, Ahmed R.
Fathallah, M-Dahmani
author_sort Ashoor, Dana
collection PubMed
description In this study, we evaluated the use of a predictive computational approach for SARS-CoV-2 genetic variations analysis in improving the current variant labeling system. First, we reviewed the basis of the system developed by the World Health Organization (WHO) for the labeling of SARS-CoV-2 genetic variants and the derivative adapted by the United States Centers for Disease Control and Prevention (CDC). Both labeling systems are based on the virus’ major attributes. However, we found that the labeling criteria of the SARS-CoV-2 variants derived from these attributes are not accurately defined and are used differently by the two agencies. Consequently, discrepancies exist between the labels given by WHO and the CDC to the same variants. Our observations suggest that giving the variant of concern (VOC) label to a new variant is premature and might not be appropriate. Therefore, we used a comparative computational approach to predict the effects of the mutations on the virus structure and functions of five VOCs. By linking these data to the criteria used by WHO/CDC for variant labeling, we ascertained that a predictive computational comparative approach of the genetic variations is a good way for rapid and more accurate labeling of SARS-CoV-2 variants. We propose to label all emergent variants, variant under monitoring or variant being monitored (VUM/VBM), and to carry out computational predictive studies with thorough comparison to existing variants, upon which more appropriate and informative labels can be attributed. Furthermore, harmonization of the variant labeling system would be globally beneficial to communicate about and fight the COVID-19 pandemic.
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spelling pubmed-93996562022-08-25 How concerning is a SARS-CoV-2 variant of concern? Computational predictions and the variants labeling system Ashoor, Dana Marzouq, Maryam Trabelsi, Khaled Chlif, Sadok Abotalib, Nasser Khalaf, Noureddine Ben Ramadan, Ahmed R. Fathallah, M-Dahmani Front Cell Infect Microbiol Cellular and Infection Microbiology In this study, we evaluated the use of a predictive computational approach for SARS-CoV-2 genetic variations analysis in improving the current variant labeling system. First, we reviewed the basis of the system developed by the World Health Organization (WHO) for the labeling of SARS-CoV-2 genetic variants and the derivative adapted by the United States Centers for Disease Control and Prevention (CDC). Both labeling systems are based on the virus’ major attributes. However, we found that the labeling criteria of the SARS-CoV-2 variants derived from these attributes are not accurately defined and are used differently by the two agencies. Consequently, discrepancies exist between the labels given by WHO and the CDC to the same variants. Our observations suggest that giving the variant of concern (VOC) label to a new variant is premature and might not be appropriate. Therefore, we used a comparative computational approach to predict the effects of the mutations on the virus structure and functions of five VOCs. By linking these data to the criteria used by WHO/CDC for variant labeling, we ascertained that a predictive computational comparative approach of the genetic variations is a good way for rapid and more accurate labeling of SARS-CoV-2 variants. We propose to label all emergent variants, variant under monitoring or variant being monitored (VUM/VBM), and to carry out computational predictive studies with thorough comparison to existing variants, upon which more appropriate and informative labels can be attributed. Furthermore, harmonization of the variant labeling system would be globally beneficial to communicate about and fight the COVID-19 pandemic. Frontiers Media S.A. 2022-08-10 /pmc/articles/PMC9399656/ /pubmed/36034694 http://dx.doi.org/10.3389/fcimb.2022.868205 Text en Copyright © 2022 Ashoor, Marzouq, Trabelsi, Chlif, Abotalib, Khalaf, Ramadan and Fathallah https://creativecommons.org/licenses/by/4.0/This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) and the copyright owner(s) are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.
spellingShingle Cellular and Infection Microbiology
Ashoor, Dana
Marzouq, Maryam
Trabelsi, Khaled
Chlif, Sadok
Abotalib, Nasser
Khalaf, Noureddine Ben
Ramadan, Ahmed R.
Fathallah, M-Dahmani
How concerning is a SARS-CoV-2 variant of concern? Computational predictions and the variants labeling system
title How concerning is a SARS-CoV-2 variant of concern? Computational predictions and the variants labeling system
title_full How concerning is a SARS-CoV-2 variant of concern? Computational predictions and the variants labeling system
title_fullStr How concerning is a SARS-CoV-2 variant of concern? Computational predictions and the variants labeling system
title_full_unstemmed How concerning is a SARS-CoV-2 variant of concern? Computational predictions and the variants labeling system
title_short How concerning is a SARS-CoV-2 variant of concern? Computational predictions and the variants labeling system
title_sort how concerning is a sars-cov-2 variant of concern? computational predictions and the variants labeling system
topic Cellular and Infection Microbiology
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9399656/
https://www.ncbi.nlm.nih.gov/pubmed/36034694
http://dx.doi.org/10.3389/fcimb.2022.868205
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