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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...
Autores principales: | , , , , , , , , , , , , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
Microbiology Society
2021
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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. |
format | Online Article Text |
id | pubmed-8743546 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2021 |
publisher | Microbiology Society |
record_format | MEDLINE/PubMed |
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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