This doctoral thesis, directed by Santiago F. Elena, analyzes the evolutionary trajectories of viruses in response to the greater or lesser susceptibility shown by their hosts. Part of the research results have been published in the journal Europhysics Letters. The thesis was defended on March 26, 2021.

RNA viruses are among the most abundant emerging pathogens. During their normal life cycle, viruses move from host to host, sometimes transmitted through the air or water, or by vectors. Within an individual host, viruses face a diversity of cellular environments and immune challenges. Viruses maximize their Darwinian biological efficiency by rapidly adapting to all of these factors. We can assume that the interaction between host genotypes and pathogen genotypes moves between two extremes. On the one hand, a pathogen genotype can infect all host genotypes and there is a universally susceptible host genotype. At the opposite extreme, infection is not possible unless there is a very precise genetic identification between the parasite and the host. This approach has revealed that infection networks have a characteristic nested structure caused by the existence of generalist viruses that infect most hosts and very permissive hosts available to most viruses. In evolutionary terms, a host with reduced susceptibility to virus infection represents strong selection on the virus population. In that case, background mortality is imposed on the mutant swarm, since most viral genotypes cannot replicate. Consequently, the effective size of the population is reduced, genetic drift becomes more important, and the fittest alleles are not necessarily fixed in the population. In hosts with higher susceptibility, the situation corresponds to weak selection, where the majority of viral genotypes are viable and contribute to the next generation. The effective size of the population is large and selection is efficient to identify the most suitable genotypes.

The main objective of the thesis “Evolution of viruses in hosts with variable susceptibility: consequences for efficacy and virulence” was to study the evolutionary response of viruses against a range of host susceptibilities. To this end, the evolution and diversification patterns of the turnip mosaic virus were studied in a collection of genotypes of the model plant Arabidopsis thaliana that differed in their susceptibility to the virus: a wild type and various mutants that had genes from the plant's resistance and defense pathways affected. The research shows that the rate of viral evolution depends on the susceptibility of the host and that generalist or specialist viral genotypes are generated depending on the degree of resistance or susceptibility of each local host.

Rebeca Navarro's thesis has been carried out in the Evolutionary and Systems Virology laboratory of the I²SysBio under the supervision of Santiago F. Elena Fito (Research Professor at the CSIC, I²SysBio). The panel was made up of Carmen Hernández Fort (IBMCP, CSIC-UPV), Ana Grande Pérez (University of Málaga) and José M. Cuevas Torrijos (I²SysBio), who rated the thesis as outstanding.