SARS-CoV-2 Variants and Their Relevant Mutational Profiles: Update Summer 2021

Since the beginning of the coronavirus disease 2019 (COVID-19) pandemic caused by it, severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has been undergoing a genetic diversification leading to the emergence of new variants. Nevertheless, a clear definition of the genetic signatures underl...

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Autores principales: Alkhatib, Mohammad, Svicher, Valentina, Salpini, Romina, Ambrosio, Francesca Alessandra, Bellocchi, Maria Concetta, Carioti, Luca, Piermatteo, Lorenzo, Scutari, Rossana, Costa, Giosuè, Artese, Anna, Alcaro, Stefano, Shafer, Robert, Ceccherini-Silberstein, Francesca
Formato: Online Artículo Texto
Lenguaje:English
Publicado: American Society for Microbiology 2021
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8597642/
https://www.ncbi.nlm.nih.gov/pubmed/34787497
http://dx.doi.org/10.1128/Spectrum.01096-21
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author Alkhatib, Mohammad
Svicher, Valentina
Salpini, Romina
Ambrosio, Francesca Alessandra
Bellocchi, Maria Concetta
Carioti, Luca
Piermatteo, Lorenzo
Scutari, Rossana
Costa, Giosuè
Artese, Anna
Alcaro, Stefano
Shafer, Robert
Ceccherini-Silberstein, Francesca
author_facet Alkhatib, Mohammad
Svicher, Valentina
Salpini, Romina
Ambrosio, Francesca Alessandra
Bellocchi, Maria Concetta
Carioti, Luca
Piermatteo, Lorenzo
Scutari, Rossana
Costa, Giosuè
Artese, Anna
Alcaro, Stefano
Shafer, Robert
Ceccherini-Silberstein, Francesca
author_sort Alkhatib, Mohammad
collection PubMed
description Since the beginning of the coronavirus disease 2019 (COVID-19) pandemic caused by it, severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has been undergoing a genetic diversification leading to the emergence of new variants. Nevertheless, a clear definition of the genetic signatures underlying the circulating variants is still missing. Here, we provide a comprehensive insight into mutational profiles characterizing each SARS-CoV-2 variant, focusing on spike mutations known to modulate viral infectivity and/or antigenicity. We focused on variants and on specific relevant mutations reported by GISAID, Nextstrain, Outbreak.info, Pango, and Stanford database websites that were associated with any clinical/diagnostic impact, according to published manuscripts. Furthermore, 1,223,338 full-length high-quality SARS-CoV-2 genome sequences were retrieved from GISAID and used to accurately define the specific mutational patterns in each variant. Finally, mutations were mapped on the three-dimensional structure of the SARS-CoV-2 spike protein to assess their localization in the different spike domains. Overall, this review sheds light and assists in defining the genetic signatures characterizing the currently circulating variants and their clinical relevance. IMPORTANCE Since the emergence of SARS-CoV-2, several recurrent mutations, particularly in the spike protein, arose during human-to-human transmission or spillover events between humans and animals, generating distinct worrisome variants of concern (VOCs) or of interest (VOIs), designated as such due to their clinical and diagnostic impacts. Characterizing these variants and their related mutations is important in tracking SAR-CoV-2 evolution and understanding the efficacy of vaccines and therapeutics based on monoclonal antibodies, convalescent-phase sera, and direct antivirals. Our study provides a comprehensive survey of the mutational profiles characterizing the important SARS-CoV-2 variants, focusing on spike mutations and highlighting other protein mutations.
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spelling pubmed-85976422021-11-18 SARS-CoV-2 Variants and Their Relevant Mutational Profiles: Update Summer 2021 Alkhatib, Mohammad Svicher, Valentina Salpini, Romina Ambrosio, Francesca Alessandra Bellocchi, Maria Concetta Carioti, Luca Piermatteo, Lorenzo Scutari, Rossana Costa, Giosuè Artese, Anna Alcaro, Stefano Shafer, Robert Ceccherini-Silberstein, Francesca Microbiol Spectr Research Article Since the beginning of the coronavirus disease 2019 (COVID-19) pandemic caused by it, severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has been undergoing a genetic diversification leading to the emergence of new variants. Nevertheless, a clear definition of the genetic signatures underlying the circulating variants is still missing. Here, we provide a comprehensive insight into mutational profiles characterizing each SARS-CoV-2 variant, focusing on spike mutations known to modulate viral infectivity and/or antigenicity. We focused on variants and on specific relevant mutations reported by GISAID, Nextstrain, Outbreak.info, Pango, and Stanford database websites that were associated with any clinical/diagnostic impact, according to published manuscripts. Furthermore, 1,223,338 full-length high-quality SARS-CoV-2 genome sequences were retrieved from GISAID and used to accurately define the specific mutational patterns in each variant. Finally, mutations were mapped on the three-dimensional structure of the SARS-CoV-2 spike protein to assess their localization in the different spike domains. Overall, this review sheds light and assists in defining the genetic signatures characterizing the currently circulating variants and their clinical relevance. IMPORTANCE Since the emergence of SARS-CoV-2, several recurrent mutations, particularly in the spike protein, arose during human-to-human transmission or spillover events between humans and animals, generating distinct worrisome variants of concern (VOCs) or of interest (VOIs), designated as such due to their clinical and diagnostic impacts. Characterizing these variants and their related mutations is important in tracking SAR-CoV-2 evolution and understanding the efficacy of vaccines and therapeutics based on monoclonal antibodies, convalescent-phase sera, and direct antivirals. Our study provides a comprehensive survey of the mutational profiles characterizing the important SARS-CoV-2 variants, focusing on spike mutations and highlighting other protein mutations. American Society for Microbiology 2021-11-17 /pmc/articles/PMC8597642/ /pubmed/34787497 http://dx.doi.org/10.1128/Spectrum.01096-21 Text en Copyright © 2021 Alkhatib et al. https://creativecommons.org/licenses/by/4.0/This is an open-access article distributed under the terms of the Creative Commons Attribution 4.0 International license (https://creativecommons.org/licenses/by/4.0/) .
spellingShingle Research Article
Alkhatib, Mohammad
Svicher, Valentina
Salpini, Romina
Ambrosio, Francesca Alessandra
Bellocchi, Maria Concetta
Carioti, Luca
Piermatteo, Lorenzo
Scutari, Rossana
Costa, Giosuè
Artese, Anna
Alcaro, Stefano
Shafer, Robert
Ceccherini-Silberstein, Francesca
SARS-CoV-2 Variants and Their Relevant Mutational Profiles: Update Summer 2021
title SARS-CoV-2 Variants and Their Relevant Mutational Profiles: Update Summer 2021
title_full SARS-CoV-2 Variants and Their Relevant Mutational Profiles: Update Summer 2021
title_fullStr SARS-CoV-2 Variants and Their Relevant Mutational Profiles: Update Summer 2021
title_full_unstemmed SARS-CoV-2 Variants and Their Relevant Mutational Profiles: Update Summer 2021
title_short SARS-CoV-2 Variants and Their Relevant Mutational Profiles: Update Summer 2021
title_sort sars-cov-2 variants and their relevant mutational profiles: update summer 2021
topic Research Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8597642/
https://www.ncbi.nlm.nih.gov/pubmed/34787497
http://dx.doi.org/10.1128/Spectrum.01096-21
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