First, at the beginning, VIROGENESIS aimed at developing software applications to foster bioinformatics analysis in clinical and epidemiological settings. VIROGENESIS has successfully contributed to the acceleration of the translation of NGS analysis results into clinical research, particularly with respect to virus discovery, identification and surveillance. Novel and fast NGS metagenomic assembly methods and virome comparison tools were developed, addressing the current lack of NGS metagenomics to characterize the 'unknown'. The tools developed with VIROGENESIS have increased precision and recall of classifications which helps in disambiguating the 'unknown' viral matter facilitating discovery and assembly of new organisms. Another important result from the VIROGENESIS project was the finding that Bayesian phylogenetic inference can be successfully used on high-throughput sequencing data. The current framework and further improvements provide, for the first time, the ability to use high precision, computationally robust Bayesian analyses on high-throughput sequencing data, improving the ability to detect the origin and spread of rapidly-evolving viruses. In addition, fast and accurate reconstruction of ancestral histories is possible for large datasets, which allows use in daily research practice of public health researchers. Software has been made open source, to be accessible, extendable and platform-independent, so their wide use and dissemination is maximized. All software has been accompanied by scientific publications describing methodology and results of testing and validation.
Second, the organisation of international workshops in Europe where a wide range of VIROGENESIS software will be used in theoretical and practical sessions strengthen the role of Europe in developing novel and innovative solutions addressing persistent challenges of NGS virome analyses. This is not only demonstrated by the impact of VIROGENESIS publications, but also by the interactions established with external partners, and with other research initiatives. Novel interactions were established to transfer knowledge and technologies from other research fields, e.g. geospatial situational awareness, into the field of epidemic tracking in order to create new opportunities.
Third, VIROGENESIS has facilitated research and innovation opportunities for SMEs as well as the commercialization of bioinformatics products. In addition to the impact initially foreseen, recent advances in VIROGENESIS technology and recent discoveries within the project have given rise to new applications, with new innovations filed in a European and US patent applications. Next, novel business opportunities for SMEs have been identified by transferring and adapting VIROGENESIS software for analyses of bacteria. By partnering with existing analysis platforms with a wide user base, VIROGENESIS will not have only guaranteed long life of the VIROGENESIS tools, but also help the open source bioinformatics suite to grow and be one of the top players as a commercial product.
Fourth, by teaching students from all over the world attending the training sessions of the highly regarded VEME workshops, these students can bring back knowledge of these tools to their own institutions, thus promoting global use. Furthermore, new methods and tools have been disseminated via a large collection of scientific publications. A VIROGENESIS pipeline tool has been implemented in the UGENE platform which will allow wide dissemination of our tool, including to researchers who computational resources and/or programming skills are modest.
