Please use this identifier to cite or link to this item: http://conacyt.repositorioinstitucional.mx/jspui/handle/1000/7836
Phylogenomics and population genomics of SARS-CoV-2 in Mexico during the pre-vaccination stage reveals variants of interest B.1.1.28.4, B.1.1.222 or B.1.1.519 and B.1.243 with mutations in the Spike protein and the Nucleocapsid
ALEJANDRA NATALI VEGA MAGAÑA
Jose Francisco Muñoz Valle
OCTAVIO PATRICIO GARCIA GONZALEZ
SOFIA BERNAL SILVA
Andreu Comas_García
Angelica Cibrian_Jaramillo
Francisco Barona Gómez
Luis Delaye
Fabien Plisson
ARELY CRUZ PEREZ
MAURICIO DIAZ SANCHEZ
CHRISTIAN A. GARCÍA-SEPÚLVEDA
Alejandro Sanchez_Flores
RAFAEL PÉREZ-ABREU
ERIK DÍAZ-VALENZUELA
Acceso Abierto
Atribución-NoComercial-SinDerivadas
https://doi.org/10.1101/2021.05.18.21256128
Understanding the evolution of SARS-CoV-2 virus in various regions of the world during the Covid19 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 RT-qPCR screening and phylogenomics reconstructions directed a sequence/structure analysis of the Spike glycoprotein, revealing 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 (VOI) 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 (SNVs) 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, so we propose an additional VOI, 20A/N:194L.V2 (B.1.243). 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.
Medrxiv
18-06-2021
Preimpreso
medrxiv.org/
VIRUS RESPIRATORIOS
Appears in Collections:Artículos científicos

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