Projects

Many new viruses, associated with different hosts or environmental samples, have been discovered during the past decade, facilitated by thewidespread adoption of metagenomics high-throughput sequencing (HTS) approaches. Characterization of these findings, including confirmed hostassociations, host range, and virulence, is lagging. This is especially true for newly discovered plant viruses from wild plants and environmentalsamples. Ecological roles of such viruses, and specifically, their potential to adapt to new hosts and possibly emerge as pathogens in agriculturalsettings are largely unknown.

Modern molecular biology tools, such as synthetic virology and mutagenesis scanning, now offer unprecedented possibilities to investigate thebiological properties and evolutionary potential of novel viruses in laboratory experimental set-ups. Advances in molecular cloning approaches enablestreamlined assembly of viral infectious clones for reverse genetics studies to investigate different aspects of virus biology, e.g., its host associations,replication rate, molecular mechanisms of its infection cycle, transmission, and its adaptive potential. The latter can be achieved by combining syntheticvirology with deep mutational scanning (DMS), a method that allows preparation of diverse mutant libraries of viral infectious clones, which can then beevolved in different conditions, to test for the effect of generated mutations on virus fitness (during e.g., adaptation to a new host). The studiesemploying such advanced experimental evolution approaches enable us to explore possible evolutionary pathways of novel viruses with unprecedentedresolution.

Within the proposed project we will bridge the gap between the discovery of new plant viruses and their characterization by preparing and employing anexperimental toolbox linking synthetic virology and modern experimental evolution approaches. We will address biological characteristics and availableevolutionary landscapes of plant viruses, newly discovered by metagenomics approaches in wild plants, environmental and archeological samples. Toachieve this, we will first (i) prepare a set of infectious viral clones for plant viruses recently discovered by metagenomics. We will then use theseinfectious viral clones to (ii) ascertain their associations with putative host plants (specifically for viruses with no clear host associations, detected inenvironmental or archaeological samples) and study their host range. Next, we will (iii) prepare deep mutational scanning libraries for a selected newlydiscovered tobamovirus and use them in (iv) experimental evolution studies addressing the adaptive constraints of this virus (what is its potential toadapt to different host plants?) and possible adaptive trade-offs (could selection for better stability of virions in environment negatively affect othertraits, such as its replicative fitness?). Finally, we will prepare a (v) protocol describing our experimental characterization toolbox to facilitate furtherresearch efforts for other discoveries.

The proposed project has the potential to make a significant impact in the field of plant virology and phytopathology by providing a toolbox for astreamlined characterization of “untamed” plant viruses. It will also bring a deeper understanding of the evolution and adaptation of plant viruses, whichis crucial for more efficient crop production and thus for addressing the increasing need for food resources due to the growing world population.

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