Genomic Evolution Strategy in SARS-CoV-2 Lineage B: Coevolution of Cis Elements

• Published in: Current Issues in Molecular Biology Vol. 46; no. 6; pp. 5744 - 5776
• Main Authors: Tamayo-Ordóñez, Yahaira de J, Rosas-García, Ninfa M, Tamayo-Ordoñez, Francisco A, Ayil-Gutiérrez, Benjamín A, Bello-López, Juan M, Sosa-Santillán, Gerardo de J, Acosta-Cruz, Erika, Anguebes-Franseschi, Francisco, Damas-Damas, Siprian, Domínguez-May, Angel V, Córdova-Quiroz, Atl Victor, Tamayo-Ordóñez, María Concepción
• Format: Journal Article
• Language: English
• Published: Switzerland MDPI AG 09.06.2024; MDPI
• Subjects: cis elements; coevolution; Coronaviruses; Health aspects; RNA; RNA structures; SARS-CoV-2; Mexico; United Kingdom; SARS-CoV-2; RNA structures; cis elements; coevolution
• ISSN: 1467-3045; 1467-3037; 1467-3045
• DOI: 10.3390/cimb46060344

In the SARS-CoV-2 lineage, RNA elements essential for its viral life cycle, including genome replication and gene expression, have been identified. Still, the precise structures and functions of these RNA regions in coronaviruses remain poorly understood. This lack of knowledge points out the need for further research to better understand these crucial aspects of viral biology and, in time, prepare for future outbreaks. In this research, the in silico analysis of the RNA structures that act in the alpha-, beta-, gamma-, and deltacoronavirus genera has provided a detailed view of the presence and adaptation of the structures of these elements in coronaviruses. The results emphasize the importance of these elements in viral biology and their variability between different viral variants. Some coronavirus variants in some groups, depending on the element (stem-loop1 and -2; pseudoknot stem-loop1 and -2, and s2m), exhibited functional adaptation. Additionally, the conformation flexibility of the s2m element in the SARS variants was determined, suggesting a coevolution of this element in this viral group. The variability in secondary structures suggests genomic adaptations that may be related to replication processes, genetic regulation, as well as the specific pathogenicity of each variant. The results suggest that RNA structures in coronaviruses can adapt and evolve toward different viral variants, which has important implications for viral adaptation, pathogenicity, and future therapeutic strategies.