Predicting the Stability of Homologous Gene Duplications in a Plant RNA Virus.

One of the striking features of many eukaryotes is the apparent amount of redundancy in coding and non-coding elements of their genomes. Despite the possible evolutionary advantages, there are fewer examples of redundant sequences in viral genomes, particularly those with RNA genomes. The factors constraining the maintenance of redundant sequences in present-day RNA virus genomes are not well known.

Efficient escape from local optima in a highly rugged fitness landscape by evolving RNA virus populations.

Predicting viral evolution has proven to be a particularly difficult task, mainly owing to our incomplete knowledge of some of the fundamental principles that drive it. Recently, valuable information has been provided about mutation and recombination rates, the role of genetic drift and the distribution of mutational, epistatic and pleiotropic fitness effects. However, information about the topography of virus' adaptive landscapes is still scarce, and to our knowledge no data has been reported so far on how its ruggedness may condition virus' evolvability.

Evaluating the within-host fitness effects of mutations fixed during virus adaptation to different ecotypes of a new host.

The existence of genetic variation for resistance in host populations is assumed to be essential to the spread of an emerging virus. Models predict that the rate of spread slows down with the increasing frequency and higher diversity of resistance alleles in the host population. We have been using the experimental pathosystem Arabidopsis thaliana-tobacco etch potyvirus (TEV) to explore the interplay between genetic variation in host's susceptibility and virus diversity.

Temporal dynamics of intrahost molecular evolution for a plant RNA virus.

Populations of plant RNA viruses are highly polymorphic in infected plants, which may allow rapid within-host evolution. To understand tobacco etch potyvirus (TEV) evolution, longitudinal samples from experimentally evolved populations in the natural host tobacco and from the alternative host pepper were phenotypically characterized and genetically analyzed. Temporal and compartmental variabilities of TEV populations were quantified using high throughput Illumina sequencing and population genetic approaches.

A viral protein mediates superinfection exclusion at the whole-organism level but is not required for exclusion at the cellular level.

Unlabelled: Superinfection exclusion (SIE), the ability of an established virus infection to interfere with a secondary infection by the same or a closely related virus, has been described for different viruses, including important pathogens of humans, animals, and plants. Citrus tristeza virus (CTV), a positive-sense RNA virus, represents a valuable model system for studying SIE due to the existence of several phylogenetically distinct strains. Furthermore, CTV allows SIE to be examined at the whole-organism level.

Onset of virus systemic infection in plants is determined by speed of cell-to-cell movement and number of primary infection foci.

The cornerstone of today's plant virology consists of deciphering the molecular and mechanistic basis of host-pathogen interactions. Among these interactions, the onset of systemic infection is a fundamental variable in studying both within- and between-host infection dynamics, with implications in epidemiology. Here, we developed a mechanistic model using probabilistic and spatio-temporal concepts to explain dynamic signatures of virus systemic infection.