RNAVIRSPE

ANALYSIS OF SPECIATION MECHANISMS IN RNA VIRUSES

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 Obiettivo del progetto (Objective)

'Parasites have high socio-economic impact due to their negative effect on humans, animals and plants welfare. Parasite evolution may lead to emergence of new infectious diseases, and compromise existing disease control strategies. Viruses are one of the most important groups of parasites causing a large fraction of emerging diseases. Adaptation to new environments may lead to population diversification, including “speciation” events resulting in the appearance of new viruses. Ecological and genetic factors are important in determining virus evolution. Environmental modifications impose selection pressures, thus changes in host population density or distribution will result in the appearance of new viral strains or species. Mutation and recombination are the main mechanisms for generating genetic variability in RNA viruses: their high mutation rates allow them to evolve rapidly adapting to new environments. Exchange of gene modules between related viral strains (modular evolution) may also result in new variants with higher fitness. We will analyze the role of these evolutionary mechanisms in the processes of virus speciation using bioinformatic tools applied to genomic sequence datasets. Analyses will focus on the families Picornaviridae, Coronaviridae and Potyviridae as models for RNA virus evolution. The three families have been widely studied, as they are important human, domestic animals and wildlife, and crop pathogens, with high sociological and agronomic relevance. Sequence data, together with information on host range and geographical distribution, are available for a large number of species and strains of these families. However, despite this data availability, to date there has been no extensive analysis of the patterns and processes of RNA virus speciation. Understanding virus evolution may be of deep interest as it may help to predict and control viral epidemics, and to understand the processes leading to the emergence of new infectious diseases.'

Introduzione (Teaser)

Both genetic and ecological factors seem to drive the evolution of viruses. By delineating the mechanisms underlying virus speciation, a European study provided important information for shaping future disease management policies.

Descrizione progetto (Article)

Viruses affect humans, animals and plants alike, thereby constituting one of the most important groups of parasites capable of causing disease. The inherent ability of viruses to adapt to new hosts and/or environments is partly responsible for the existence of so many viral species. However, the precise mechanisms underlying such speciation events are not clear.

To shed light on virus evolution, the EU-funded 'Analysis of speciation mechanisms in RNA viruses' (RNAVIRSPE) project analysed the contribution of various ecological factors. These were coupled with assessment of mutation rates, and gene expression profiles in three animal viruses and three plant virus groups. The rationale was that such analyses, apart from being scientifically informative, would provide insight into the emergence of important pathogens.

Using state-of-the-art bioinformatics tools, scientists analysed large datasets of genomic sequences and generated phylogenetic reconstructions. Results indicated some viruses had congruent phylogenies with their hosts, but all the analysed viruses evolved at higher rates than their host. This suggests that adaptation to the host rather than host-virus co-divergence influences virus evolution.

Interestingly, host migration was suggested as another driver of virus speciation. With the HIV epidemic in the Caribbean as an example, researchers could associate the genetic structure of a virus population with the country of origin. Human intervention and landscape heterogeneity also affect virus diversification, probably driven by the need to adapt to the new environment.

Apart from ecological factors, it became evident that certain genetic factors could also mediate evolution of viruses. RNA viruses with overlapping genes exhibited reduced ability to generate new variants and form new species. The targeting of slow-evolving genes could, therefore, be utilised to increase the durability of vaccine-mediated protection.

The information generated during RNAVIRSPE could be adapted to prevent the development of drug-resistant viral strains. Furthermore, to design efficient control strategies for viral diseases, the main viral host and its migration routes should be considered alongside the availability of alternative hosts.