Assembly of positive-sense single-stranded RNA viruses occurs in the cytoplasm. These viruses must selectively package their genomic RNA (gRNA) from a pool of cellular and viral RNAs. In other words, the viral capsid proteins must select the correct RNA from a heterologous RNA population.

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      Mayra Colunga-Saucedo, as part of her Ph.D. thesis, designed a helper/replicon cDNA system and fully infectious clones (CHIKV 181/25 with mKate2 as a reporter gene) in plasmids for mammalian expression. These plasmids allow us to study the assembly of the core and virion budding. Also, we are interested in studying the mechanics of the budding process (collaborations with Profs. Tuli Mukhopadhyay and R. Zandi) and the role of the interactions between the glycoproteins in this process. In fact, a multidisciplinary approach combining physical and molecular virology has led us to propose novel protein-protein interactions that are key to viral particle budding at the plasma membrane.

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Most of our group focuses on understanding the interactions that control the assembly of the Old-World Alphavirus Chikungunya. To do this, we have focused on combining available cryo-EM data with evolutionary analysis to identify hosts. These ​hotspots are highly conserved sites in Old-World Alphaviruses, and, in some cases, in all Alphaviruses, that most likely play a role in assembly and disassembly. 

      Our first analysis focused on the interaction between the capsid protein, which most likely controls capsomer assembly, and its interactions. This was done by combining structural and evolutionary analyses, allowing us to propose multiple interaction hotspots and the mechanisms by which these interactions arose during the early evolution of Alphaviruses. This part of the project has been led by two undergraduate students, Carolina Piña-Ruiz and Luis Ruben Rocha-Jaime, and is a collaboration with Drs. Juan Carlos Muñoz-Escalante, Roger Castells-Graells, and Roya Zandi. This project has allowed us to propose a new evolutionary pathway for these viruses and to examine their implications for pathogenicity.

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      Now, we have three more undergraduate students studying the role of these amino acids on virion stability, assembly, and morphology (Edgar Mota-Media, Diana Zúñiga-Izaguirre, and Italia Rivera-Martínez).

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      Finally, we have two Ph.D. students (Andrea Castorena-Robles and Miguel Ángel Coronado-Ipiña) who have used this same combination of structural and evolutionary approaches to study the interactions between the glycoproteins (E1-E2, and E2-E2', respectively) that drive assembly and disassembly.

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Thin-section TEM micrograph of CHIKV 181/25 budding from an infected cell (our archive).

 

Update: November 2025

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