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Phylogenomics and population genomics of SARS-CoV-2 in Mexico during the pre-vaccination stage reveals variants of interest B.1.1.28.4 and B.1.1.222 or B.1.1.519 and the nucleocapsid mutation S194L associated with symptoms

Understanding the evolution of the SARS-CoV-2 virus in various regions of the world during the Covid-19 pandemic is essential to help mitigate the effects of this devastating disease. We describe the phylogenomic and population genetic patterns of the virus in Mexico during the pre-vaccination stage...

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Autores principales: Barona-Gómez, Francisco, Delaye, Luis, Díaz-Valenzuela, Erik, Plisson, Fabien, Cruz-Pérez, Arely, Díaz-Sánchez, Mauricio, García-Sepúlveda, Christian A., Sanchez-Flores, Alejandro, Pérez-Abreu, Rafael, Valencia-Valdespino, Francisco J., Vega-Magaña, Natali, Muñoz-Valle, José Francisco, García-González, Octavio Patricio, Bernal-Silva, Sofía, Comas-García, Andreu, Cibrián-Jaramillo, Angélica
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Microbiology Society 2021
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8743546/
https://www.ncbi.nlm.nih.gov/pubmed/34846283
http://dx.doi.org/10.1099/mgen.0.000684
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author Barona-Gómez, Francisco
Delaye, Luis
Díaz-Valenzuela, Erik
Plisson, Fabien
Cruz-Pérez, Arely
Díaz-Sánchez, Mauricio
García-Sepúlveda, Christian A.
Sanchez-Flores, Alejandro
Pérez-Abreu, Rafael
Valencia-Valdespino, Francisco J.
Vega-Magaña, Natali
Muñoz-Valle, José Francisco
García-González, Octavio Patricio
Bernal-Silva, Sofía
Comas-García, Andreu
Cibrián-Jaramillo, Angélica
author_facet Barona-Gómez, Francisco
Delaye, Luis
Díaz-Valenzuela, Erik
Plisson, Fabien
Cruz-Pérez, Arely
Díaz-Sánchez, Mauricio
García-Sepúlveda, Christian A.
Sanchez-Flores, Alejandro
Pérez-Abreu, Rafael
Valencia-Valdespino, Francisco J.
Vega-Magaña, Natali
Muñoz-Valle, José Francisco
García-González, Octavio Patricio
Bernal-Silva, Sofía
Comas-García, Andreu
Cibrián-Jaramillo, Angélica
author_sort Barona-Gómez, Francisco
collection PubMed
description Understanding the evolution of the SARS-CoV-2 virus in various regions of the world during the Covid-19 pandemic is essential to help mitigate the effects of this devastating disease. We describe the phylogenomic and population genetic patterns of the virus in Mexico during the pre-vaccination stage, including asymptomatic carriers. A real-time quantitative PCR screening and phylogenomic reconstructions directed at sequence/structure analysis of the spike glycoprotein revealed mutation of concern E484K in genomes from central Mexico, in addition to the nationwide prevalence of the imported variant 20C/S:452R (B.1.427/9). Overall, the detected variants in Mexico show spike protein mutations in the N-terminal domain (i.e. R190M), in the receptor-binding motif (i.e. T478K, E484K), within the S1–S2 subdomains (i.e. P681R/H, T732A), and at the basis of the protein, V1176F, raising concerns about the lack of phenotypic and clinical data available for the variants of interest we postulate: 20B/478K.V1 (B.1.1.222 or B.1.1.519) and 20B/P.4 (B.1.1.28.4). Moreover, the population patterns of single nucleotide variants from symptomatic and asymptomatic carriers obtained with a self-sampling scheme confirmed the presence of several fixed variants, and differences in allelic frequencies among localities. We identified the mutation N:S194L of the nucleocapsid protein associated with symptomatic patients. Phylogenetically, this mutation is frequent in Mexican sub-clades. Our results highlight the dual and complementary role of spike and nucleocapsid proteins in adaptive evolution of SARS-CoV-2 to their hosts and provide a baseline for specific follow-up of mutations of concern during the vaccination stage.
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spelling pubmed-87435462022-01-10 Phylogenomics and population genomics of SARS-CoV-2 in Mexico during the pre-vaccination stage reveals variants of interest B.1.1.28.4 and B.1.1.222 or B.1.1.519 and the nucleocapsid mutation S194L associated with symptoms Barona-Gómez, Francisco Delaye, Luis Díaz-Valenzuela, Erik Plisson, Fabien Cruz-Pérez, Arely Díaz-Sánchez, Mauricio García-Sepúlveda, Christian A. Sanchez-Flores, Alejandro Pérez-Abreu, Rafael Valencia-Valdespino, Francisco J. Vega-Magaña, Natali Muñoz-Valle, José Francisco García-González, Octavio Patricio Bernal-Silva, Sofía Comas-García, Andreu Cibrián-Jaramillo, Angélica Microb Genom Research Articles Understanding the evolution of the SARS-CoV-2 virus in various regions of the world during the Covid-19 pandemic is essential to help mitigate the effects of this devastating disease. We describe the phylogenomic and population genetic patterns of the virus in Mexico during the pre-vaccination stage, including asymptomatic carriers. A real-time quantitative PCR screening and phylogenomic reconstructions directed at sequence/structure analysis of the spike glycoprotein revealed mutation of concern E484K in genomes from central Mexico, in addition to the nationwide prevalence of the imported variant 20C/S:452R (B.1.427/9). Overall, the detected variants in Mexico show spike protein mutations in the N-terminal domain (i.e. R190M), in the receptor-binding motif (i.e. T478K, E484K), within the S1–S2 subdomains (i.e. P681R/H, T732A), and at the basis of the protein, V1176F, raising concerns about the lack of phenotypic and clinical data available for the variants of interest we postulate: 20B/478K.V1 (B.1.1.222 or B.1.1.519) and 20B/P.4 (B.1.1.28.4). Moreover, the population patterns of single nucleotide variants from symptomatic and asymptomatic carriers obtained with a self-sampling scheme confirmed the presence of several fixed variants, and differences in allelic frequencies among localities. We identified the mutation N:S194L of the nucleocapsid protein associated with symptomatic patients. Phylogenetically, this mutation is frequent in Mexican sub-clades. Our results highlight the dual and complementary role of spike and nucleocapsid proteins in adaptive evolution of SARS-CoV-2 to their hosts and provide a baseline for specific follow-up of mutations of concern during the vaccination stage. Microbiology Society 2021-11-30 /pmc/articles/PMC8743546/ /pubmed/34846283 http://dx.doi.org/10.1099/mgen.0.000684 Text en © 2021 The Authors https://creativecommons.org/licenses/by/4.0/This is an open-access article distributed under the terms of the Creative Commons Attribution License.
spellingShingle Research Articles
Barona-Gómez, Francisco
Delaye, Luis
Díaz-Valenzuela, Erik
Plisson, Fabien
Cruz-Pérez, Arely
Díaz-Sánchez, Mauricio
García-Sepúlveda, Christian A.
Sanchez-Flores, Alejandro
Pérez-Abreu, Rafael
Valencia-Valdespino, Francisco J.
Vega-Magaña, Natali
Muñoz-Valle, José Francisco
García-González, Octavio Patricio
Bernal-Silva, Sofía
Comas-García, Andreu
Cibrián-Jaramillo, Angélica
Phylogenomics and population genomics of SARS-CoV-2 in Mexico during the pre-vaccination stage reveals variants of interest B.1.1.28.4 and B.1.1.222 or B.1.1.519 and the nucleocapsid mutation S194L associated with symptoms
title Phylogenomics and population genomics of SARS-CoV-2 in Mexico during the pre-vaccination stage reveals variants of interest B.1.1.28.4 and B.1.1.222 or B.1.1.519 and the nucleocapsid mutation S194L associated with symptoms
title_full Phylogenomics and population genomics of SARS-CoV-2 in Mexico during the pre-vaccination stage reveals variants of interest B.1.1.28.4 and B.1.1.222 or B.1.1.519 and the nucleocapsid mutation S194L associated with symptoms
title_fullStr Phylogenomics and population genomics of SARS-CoV-2 in Mexico during the pre-vaccination stage reveals variants of interest B.1.1.28.4 and B.1.1.222 or B.1.1.519 and the nucleocapsid mutation S194L associated with symptoms
title_full_unstemmed Phylogenomics and population genomics of SARS-CoV-2 in Mexico during the pre-vaccination stage reveals variants of interest B.1.1.28.4 and B.1.1.222 or B.1.1.519 and the nucleocapsid mutation S194L associated with symptoms
title_short Phylogenomics and population genomics of SARS-CoV-2 in Mexico during the pre-vaccination stage reveals variants of interest B.1.1.28.4 and B.1.1.222 or B.1.1.519 and the nucleocapsid mutation S194L associated with symptoms
title_sort phylogenomics and population genomics of sars-cov-2 in mexico during the pre-vaccination stage reveals variants of interest b.1.1.28.4 and b.1.1.222 or b.1.1.519 and the nucleocapsid mutation s194l associated with symptoms
topic Research Articles
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8743546/
https://www.ncbi.nlm.nih.gov/pubmed/34846283
http://dx.doi.org/10.1099/mgen.0.000684
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