%0 Journal Article %A Barona-Gómez, Francisco %A Delaye, Luis %A Díaz-Valenzuela, Erik %A Plisson, Fabien %A Cruz-Pérez, Arely %A Díaz-Sánchez, Mauricio %A García-Sepúlveda, Christian A. %A Sanchez-Flores, Alejandro %A Pérez-Abreu, Rafael %A Valencia-Valdespino, Francisco J. %A Vega-Magaña, Natali %A Muñoz-Valle, José Francisco %A García-González, Octavio Patricio %A Bernal-Silva, Sofía %A Comas-García, Andreu %A Cibrián-Jaramillo, Angélica %T 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 %D 2021 %J Microbial Genomics, %V 7 %N 11 %@ 2057-5858 %C 000684 %R https://doi.org/10.1099/mgen.0.000684 %K nucleocapsid %K SARS-CoV-2 %K population genomics %K Mexico %K variants %K asymptomatic %I Microbiology Society, %X 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. %U https://www.microbiologyresearch.org/content/journal/mgen/10.1099/mgen.0.000684