Friday, 22nd September 2017

Virology and Microbiology

                Genetic variability of RNA viruses




Esteban Domingo Solans




Research summary:

We have worked in the development of new antiviral strategies based on lethal mutagenesis to avoid selection of treatment-escape viral mutants. The work has had an experimental part with hepatitis C virus (HCV) and foot-and-mouth disease virus (FMDV), as well as a theoretical line on new biological implications of quasispecies dynamics. With HCV we have documented that high viral fitness can confer partial resistance to the polymerase inhibitor sofosbuvir. In a search for new mutagenic agents licensed for administration to humans, we have shown that the broad-spectrum antiviral agent sofosbuvir is mutagenic for HCV. The cell culture system for HCV has allowed us several collaborations with other groups on virus-cell interactions. Regarding FMDV, we have identified polymerase residues that affect nucleotide analogue recognition; this knowledge may permit the design of more effective antiviral combinations. We have described a lethal mutagenesis-escape mechanism which is polymerase-independent and is associated with a single amino acid substitution in non-structural viral protein 2C. We have adopted for our studies measurements of diversity derived from deep sequencing and have participated in the design of microarrays to detect minority variants in viral populations.

Regarding theoretical studies, we have compiled quasispecies implications revealed by others and us, with publication of two books and several articles. In one of them we propose a distinction between recombination which is mechanistically unavoidable and biologically relevant recombination that signals important transition points in an evolution which is essentially clonal. Our efforts are directed towards converting a theoretical body of quasispecies understanding into applications to combat viral diseases.




Serial passages of hepatitis C virus (HCV) in human hepatoma cells (Huh 7.5)
in the absence or presence of increasing concentrations of interferon-α (IFN-α).
Low, Med, High represent 3 evolutionary lines with a different initial IFN-α concentration.
Details of this study are in Perales et al. J. Virol., 87(13), 7593-7607, 2013.



Relevant publications:


  • Domingo, E., Sheldon, J. and Perales, C. (2012). Viral quasispecies evolution. Microbiology and Molecular Biology Reviews, 76, (2)159-216.
  • Perales, C. Moreno, E. Domingo, E. (2015). Clonality and intracellular polyploidy in virus evolution and pathogenesis. Proc Natl Acad Sci USA, 112(29):8887-92.
  • Andino, R. and Domingo, E. (2015). Viral quasispecies. Virology, 479-480: 46-51.
  • Perales, C. Moreno, E. Domingo, E. (2015). Clonality and intracellular polyploidy in virus evolution and pathogenesis. Proc Natl Acad Sci USA, 112(29):8887-92.
  • Ferrer-Orta, C., de la Higuera, I., Caridi, F., Sanchez-Aparicio, M.T., Moreno, E. Perales, C., Singh, K., Sarafianos, S.G., Sobrino, F. Domingo, E., Verdaguer, N. (2015). Multifunctionality of a picornavirus polymerase domain: nuclear localization signal and nucleotide recognition. J. Virol., 89(13):6848-6859.
  • Madejón, A., Sheldon, J., Francisco-Recuero, I., Perales, C., Dominguez-Beato, M., Lasa, M., Sanchez-Perez, I., Muntané, J., Domingo, E., Garcia-Samaniego, J., Sanchez-Pacheco, A. (2015). Hepatitis C virus-mediated Aurora B kinase inhibition modulates inflammatory pathway and viral infectivity. Journal of Hepatology, 63(2): 312-9.
  • Perez-del-Pulgar, S., Gregori, J., Rodriguez-Frias, F., Gonzalez, P., García-Cehic, D., Ramirez, S., Casillas, R., Domingo, E., Esteban, J. I., Forns, X., Quer, J. (2015). Quasispecies dynamics in hepatitis C liver transplant recipients receiving grafts from hepatitis C virus infected donors. J. Gen. Virol., 96:3493-3498.
  • Domingo, E. Perales, C. (2016). Viral quasispecies and lethal mutagenesis. European Review, 24(1):39-48.
  • Domingo, E. Perales, C. (2016). Species Concepts: Viral quasispecies. In: Kliman, R.M. (ed.), Encyclopedia of Evolutionary Biology, vol.4, pp. 228-235. Oxford: Academic Press.
  • Perales, C., Quer, J., Gregori, J., Esteban, J.I., Domingo, E. (2015). Resistance of hepatitis C virus to inhibitors: complexity and clinical implications. Viruses, 7:5746-5766.
  • Domingo, E. (2016). Virus as Populations. Composition, complexity, dynamics and biological implications. Academic Press, Elsevier, Amsterdam.
  • Domingo, E., Schuster, P. (eds.) (2016). Quasispecies: From Theory to Experimental Systems. Curr. Top. Microbiol. Immunol., vol.392. Switzerland: Springer.
  • Domingo, E., Schuster, P. (2016). What is a quasispecies? Historical origins and current scope. Curr. Top. Microbiol. Immunol., 392:1-22.
  • Perales, C., Domingo, E. (2016). Antiviral strategies based on lethal mutagenesis and error threshold. Curr. Top. Microbiol. Immunol., 392:323-339.
  • Gregori, J., Perales, C., Rodríguez-Frías, F., Esteban, J.I., Quer, J., Domingo, E. (2016). Viral Quasispecies Complexity M
  • Valero, M.L., Sabariegos, R., Cimas, F., Perales, C., Domingo, E., Sánchez-Prieto, R., Mas, A. (2016). HCV RNA-dependent RNA polymerase interacts with Akt/PKB inducing its subcellular re-localization. Antimicrob. Agents Chemother., 60(6):3540-3550.
  • Gallego, I., Sheldon, J., Moreno, E., Gregori, J., Quer, J., Esteban. J.I., Rice, C.M., Domingo, E., Perales, C. (2016). Barrier-Independent, Fitness-Associated Diferences in Sofosbuvir Efficacy against Hepatitis C virus. Antimicrob. Agents Chemother., 60(6):3786-3793.
  • Agudo, R., de la Higuera, I., Arias, A., Grande-Perez, A., Domingo, E. (2016). Involvement of a joker mutation in a polymerase-independent lethal mutagenesis escape mechanism. Virology 494:257-266.
  • De Ávila, A.I., Gallego, I., Soria, M.E., Gregori, J., Quer, J., Esteban, J.I., Rice, C.M., Domingo, E., Perales, C. (2016).Lethal mutagenesis of hepatitis C virus induced by favipiravir  .PLoS ONE, 11 (10): e0164691.
  • Martín, V., Perales, C., Fernández-Algar, M., Dos Santos, HG., Garrido, P., Pernas, M., Parro, V., Moreno, M., García-Pérez, J., Alcamí, J., Torán, JL., Abia, D., Domingo, E., Briones, C. (2016). An Efficient Microarray-Based Genotyping Platform for the Identification of Drug-Resistance Mutations in Majority and Minority Subpopulations of HIV-1 Quasispecies. PLoS ONE, 11(12):e0166902.
  • Sobrino, F. and Domingo, E. (eds.) (2017). “Foot-and-Mouth Disease Virus: Current Research and Emerging Trends”, Horizon Scientific Press – Caister Academic Press, Poole, UK.
  • Domingo, E., de la Higuera, I., Moreno, E., de Ávila, A.I., Agudo, R., Arias, A., Perales, C. (2017). Quasispecies dynamics taught by natural and experimental evolution of foot-and-mouth disease virus. In: F. Sobrino and E. Domingo (Eds.). Foot-and-Mouth Disease Virus: Current Research and Emerging Trends, Horizon Scientific Press – Caister Academic Press, Poole, UK, pp. 147-170.
  • de Avila, A. I.; Moreno, E.; Perales, C.; Domingo, E. (2017). Favipiravir can evoke lethal mutagenesis and extinction of foot-and-mouth disease virus. Virus Res., 233, 105-112.
  • Moreno, E.; Gallego, I.; Gregori, J.; Lucia-Sanz, A.; Soria, M. E.; Castro, V.; Beach, N. M.; Manrubia, S.; Quer, J.; Esteban, J. I.; Rice, C. M.; Gomez, J.; Gastaminza, P.; Domingo, E.; Perales, C. (2017). Internal Disequilibria and Phenotypic Diversification during Replication of Hepatitis C Virus in a Noncoevolving Cellular Environment. J. Virol., 91 (10), e02505-16.
  • de la Higuera, I.; Ferrer-Orta, C.; de Avila, A. I.; Perales, C.; Sierra, M.; Singh, K.; Sarafianos, S. G.; Dehouck, Y.; Bastolla, U.; Verdaguer, N.; Domingo, E. (2017). Molecular and Functional Bases of Selection against a Mutation Bias in an RNA Virus. Genome Biol. Evol., 9 (5), 1212-1228.



  • N. Sevilla, E. Domingo, C. Escarmís, S. Ojosnegros, J. García-Arriaza, M. Sanz-Rojo, T. Rodríguez. "Vacuna atenuada para la fiebre aftosa". Nº DE SOLICITUD: P200801583. Patente concedida en España el 16/06/2011. Nº PUB: ES2344875.



Doctoral Theses:

  • Héctor Moreno Borrero (2012).  Dinámica poblacional del virus de la coriomeningitis linfocitaria ratón en su interacción con agentes mutagénicos. Universidad Autónoma de Madrid. Directors: Esteban Domingo y Verónica Martín.
  • Ignacio de la Higuera Hernández (2014). Factores determinantes del reconocimiento de nucleótidos en el virus de la fiebre aftosa. Universidad Autónoma de Madrid. Director: Esteban Domingo.
  • Ana Mª Ortega Prieto (2014). Mutagénesis letal del virus de la Hepatitis C. Universidad Autónoma de Madrid. Directors: Esteban Domingo y Celia Perales.
  • Elena Moreno del Olmo (2017). Evolución a largo plazo de virus RNA en ambiente bilógico constante. Universidad Autónoma de Madrid. Directors: Esteban Domingo y Celia Perales.



Other Activities:

  • Académico Numerario de la Real Academia de Ciencias Exactas, Físicas y Naturales, adscrito a la Sección de Ciencias Naturales, (2011).
  • Miembro de la Red Española de Biofísica, coordinada por el Dr. David Reguera, desde 2011.
  • Miembro del Global Virology Network, coordinado por el Dr. Robert Gallo, desde 2011.
  • Miembro del Comité Organizador del Congreso FEMS 2011 (Ginebra, Suiza, 2011).
  • Editor asociado de la revista Virus Research desde 2012.