Chikungunya virus assembly and budding
Positive-sense single-stranded RNA viruses assemble 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.
As part of her Ph.D. thesis, Mayra Colunga-Saucedo 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 core assembly and virion budding. We are also interested in studying the mechanics of budding (in collaboration with Profs. Tuli Mukhopadhyay and R. Zandi) and the role of 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.
Most of our group focuses on understanding the interactions that control the assembly of the Old-World Alphavirus Chikungunya. To do this, we combine 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 capsid protein, which most likely controls capsomer assembly, and its interactions. We did this 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.
Now, we have three more undergraduate students studying the role of these amino acids in virion stability, assembly, and morphology (Edgar Mota-Media, Diana Zúñiga-Izaguirre, and Italia Rivera-Martínez).
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.
Thin-section TEM micrograph of CHIKV 181/25 budding from an infected cell (our archive).
Published articles on this topic:
1. Zhang, S., Li. S., Coronado-Ipiña, M.A., Comas-Garcia, M., Gopinathan, A., van der Schoot, P., and Zandi, R. (2026) Mechanisms of Viral Budding Through Cellular Membranes. Journal of Chemical Physics 165, 094112
2. Piña-Ruiz, W.C.$, Jaime-Rocha, L.R.$, Castorena-Robles, A., Castells-Graells, R., Zandi, R., Muñoz-Escalante, J.C.*, Comas-Garcia, M*. (2026) Highly conserved core residues define Old-World Alphaviruses and trace early evolutionary divergence. Journal of Molecular Evolution. 94, 668–685
3. Coronado-Ipiña, M.A.$, Zhang, S.$, Siyu, L., Hernández-Sánchez, P., Cadena-Lopez, D., Labrada-Martagon, V., Gopinathan, A., Mukhopadhyay, S., Zandi, R*., Comas-Garcia, M.* Multiple protein-protein interactions drive the assembly and budding of the Chikungunya virion. (2026) ACS Infectious Diseases 12 (7), 2383–2395 IF: 3.8
4. Comas-García, M, Revisiting Alphavirus RNA packaging and assembly: a complex story with multiple angles. (2026) FEBS Letters In press
5. Comas-Garcia, M. (2024), How structural biology has changed our understanding of icosahedral viruses. Journal of Virology. e01111-23
6. Colunga-Saucedo, M., Rubio-Hernandez, E.I., Coronado-Ipiña, M.A., Rosales-Mendoza, S., Castillo-Martin del Campo, C.G., Comas-Garcia, M.* (2023) Construction of a Chikungunya virus, replicon, and helper plasmids for transfection of mammalian cells. Viruses. 15(1).132 IF: 3.5
Update: November 2026
