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Molecular transition of SARS-CoV-2 from critical patients during the first year of the COVID-19 pandemic in Mexico City

2023; Frontiers Media; Volume: 13; Linguagem: Inglês

10.3389/fcimb.2023.1155938

2235-2988

Aldo Hugo De La Cruz-Montoya, Clara Estela Díaz Velásquez, Héctor Martínez-Gregorio, Miguel Ruiz-De La Cruz, José Bustos‐Arriaga, Tannya Castro-Jiménez, Jonadab E. Olguín, Miriam Rodríguez‐Sosa, Luis Ignacio Terrazas-Valdés, Luis Jiménez-Álvarez, Nora E. Regino-Zamarripa, Gustavo Ramírez-Martínez, Alfredo Cruz‐Lagunas, Irlanda Peralta‐Arrieta, Leonel Armas‐López, Belinda Maricela Contreras-Garza, Gabriel Palma-Cortés, Carlos Cabello-Gutiérrez, Renata Báez-Saldaña, Joaquı́n Zúñiga, Federico Ávila‐Moreno, Felipe Vaca‐Paniagua,

CRISPR and Genetic Engineering

Background The SARS-CoV-2 virus has caused unprecedented mortality since its emergence in late 2019. The continuous evolution of the viral genome through the concerted action of mutational forces has produced distinct variants that became dominant, challenging human immunity and vaccine development. Aim and methods In this work, through an integrative genomic approach, we describe the molecular transition of SARS-CoV-2 by analyzing the viral whole genome sequences from 50 critical COVID-19 patients recruited during the first year of the pandemic in Mexico City. Results Our results revealed differential levels of the evolutionary forces across the genome and specific mutational processes that have shaped the first two epidemiological waves of the pandemic in Mexico. Through phylogenetic analyses, we observed a genomic transition in the circulating SARS-CoV-2 genomes from several lineages prevalent in the first wave to a dominance of the B.1.1.519 variant (defined by T478K, P681H, and T732A mutations in the spike protein) in the second wave. Conclusion This work contributes to a better understanding of the evolutionary dynamics and selective pressures that act at the genomic level, the prediction of more accurate variants of clinical significance, and a better comprehension of the molecular mechanisms driving the evolution of SARS-CoV-2 to improve vaccine and drug development.