| Autor: |
Barona-Gómez F; Unidad de Genómica Avanzada (Langebio), Cinvestav-IPN, Irapuato, Guanajuato, Mexico., Delaye L; Departamento de Ingeniería Genética, Unidad Irapuato, Cinvestav-IPN, Irapuato, Guanajuato, México., Díaz-Valenzuela E; Unidad de Genómica Avanzada (Langebio), Cinvestav-IPN, Irapuato, Guanajuato, Mexico., Plisson F; Conacyt - Unidad de Genómica Avanzada (Langebio), Cinvestav-IPN, Irapuato, Guanajuato, México., Cruz-Pérez A; Unidad de Genómica Avanzada (Langebio), Cinvestav-IPN, Irapuato, Guanajuato, Mexico., Díaz-Sánchez M; Molecular Biology Research & Development Department, GrupoT, Irapuato, Guanajuato, México., García-Sepúlveda CA; Facultad de Medicina, Universidad Autónoma de San Luis Potosí, San Luis, San Luis Potosí, México., Sanchez-Flores A; Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, Morelos, México., Pérez-Abreu R; Centro de Investigación en Matemáticas AC (Cimat), Sede Aguascalientes, Aguascalientes, México., Valencia-Valdespino FJ; Prothesia, Monterrey, Nuevo Leon, México., Vega-Magaña N; Laboratory for the Diagnosis of Emerging and Reemerging Diseases (LaDEER), University Center for Health Sciences, University of Guadalajara, Guadalajara, Jalisco, México., Muñoz-Valle JF; Institute for Research in Biomedical Sciences, University Center for Health Sciences, University of Guadalajara, Guadalajara, Jalisco, México., García-González OP; Molecular Biology Research & Development Department, GrupoT, Irapuato, Guanajuato, México., Bernal-Silva S; Centro de Investigación en Ciencias de la Salud y Biomedicina, Universidad Autónoma de San Luis Potosí, San Luis, San Luis Potosí, México., Comas-García A; Centro de Investigación en Ciencias de la Salud y Biomedicina, Universidad Autónoma de San Luis Potosí, San Luis, San Luis Potosí, México.; Facultad de Medicina, Universidad Autónoma de San Luis Potosí, San Luis, San Luis Potosí, México., Cibrián-Jaramillo A; Unidad de Genómica Avanzada (Langebio), Cinvestav-IPN, Irapuato, Guanajuato, Mexico. |
| Abstrakt: |
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. |
