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Virus-X: Viral Metagenomics for Innovation Value

Periodic Reporting for period 1 - Virus-X (Virus-X: Viral Metagenomics for Innovation Value)

Reporting period: 2016-04-01 to 2017-09-30

The Virus-X project is designed to explore and access the genomes of natural viruses, study their diversity and impact in extreme ecosystems, and determine functional roles and the potential of encoded gene products for biotechnological applications. The research and development program employs metagenomics (using collection of genes extracted from environmental samples) and sequence-based bio-prospecting methodologies for accessing this diverse environmental genetic material, combining bioinformatics, functional analysis and 3D structure determination of gene products. The Virus-X project puts emphasis on developing new tools to strengthen future efforts in the field of metagenomics. This includes new bioinformatics tools for sequence analysis and structure-function analysis of protein families. The Virus-X project will enhance the understanding of microbial communities and functional dynamics between viruses and microorganisms. The exploration of viruses in natural cold ecosystems in the ocean off the coast of Norway, hydrothermal vents on the North Atlantic ridge and geothermal areas (hot springs) in Iceland is the main focus in the Virus-X project.

The overall objectives in this multidisciplinary project includes both scientific and technological objectives. Among the scientific objectives are better understanding of microbial ecosystems, the diversity of viruses in nature and their interaction with their natural microbial hosts. Of special interest in understanding virus-host interactions are instruments of immunity in bacteria against viruses. Such instruments are for instance the basis for the CRISPR system discovery and a technology that is proving to have tremendous societal value already. Also of outmost importance in this project is the elucidation of the function of gene products that hitherto have unknown function. The metagenomics approach, combined with the development of powerful new bioinformatics tools, structural determinations of gene products and complementary biochemical analysis may provide a way for such scientific discoveries.

Enzymes from bacteria and viruses have before proved to be of immense value and are the tools that have enabled the revolution we have witnessed in biotechnology, genetics and other biological sciences. Not the least are some of the most important tools, for instance heat stable DNA polymerases for use in a Polymerase Chain Reaction (PCR), derived from microorganisms that live under extreme environmental conditions. Such environments, hot springs and geothermal ecosystems, are a special focus point for the Virus-X project for the exploration and exploitation of the genetic diversity within the genomes of the viral world. Virus-X is a research and development plan ultimately leading to innovations and industrial value in the form of specific marketable products of viral origin, i.e. biocatalysts (enzymes) for biotech applications, as well as improved services in the field of bioinformatics and structural biology.
As the Virus-X project is built up as a bio-discovery pipeline fed by genetic resources from microbial ecosystems, the initial phase in the project has focused on environmental sampling for processing and extraction of DNA for subsequent sequencing and analysis of the genetic data. A set of genes in the genomic data have been selected as targets and cloning, expression and purification of the corresponding gene products is underway in several laboratories in the Virus-X consortium. Biochemical analysis and determination of 3D structures of selected gene products as one of the last steps in the bio-discovery pipeline have already been initiated with the first structure of viral protein being determined within the first 18 months of the Virus-X project.
The Virus-X project will open up doors to previously unexplored genetic diversity with a large number of genes from the genomes of viruses being targeted for analysis and exploitation. It is expected that the project will facilitate the development of gene products that are both useful and commercially valuable for industry with corresponding societal implications. The project will also have the potential for discovery of exciting new biological functions by elucidating the function of gene products with previously unknown function using methods of bioinformatics, crystal structure determination and complementary biochemical characterization. The approach will also promote further development of methods and tools in the field for the benefit of future explotations of natural genetic resources. The scientific impact of the project also includes clearer understanding of microbial communities and discovery of novel genes and proteins. The project is expected to have major impact in numerous areas: exploration of new genetic territory and sequence diversity, development of new approaches and tools for metagenomics, understanding of microbial communities and identification of commercially useful genes with corresponding impact on the European biotech industry towards new marketable products and services. A scientific undertaking of this scale is however only possible through substantial funding, in this case from the European Horizon 2020 research and innovation program.