Facilitating plant virus surveillance: integrated data management and analysis for epidemic studies

International audience

English. In recent years, the tracking of emerging viral pathogens has greatly benefited from high throughput sequencing data. This technology enables early detection of variants of interest and concern while also helping to identify factors influencing viral spread. However, leveraging sequencing data for broader research presents several challenges, including centralized data management, standardized epidemiological annotations, controlled access within organizations or consortia, and user-friendly bioinformatics tools for analysis. Genome Detective (www.genomedetective.com) is a web-based platform that provides such an integrated solution for managing sequencing data. It was successfully employed to trace virus outbreaks during the recent SARS-CoV-2 epidemics. We will demonstrate how it has been successfully utilized in the Horizon 2020 project VIRTIGATION (www.virtigation.eu) to study ongoing ToBRFV and ToLCNDV epidemics. The platform allows members to submit their data to a centralized yet private database, ensuring secure storage and controlled access. Additionally, it employs robust algorithms to analyze multiple samples from different consortium members, generating standardized and comparable reports across institutions. Researchers can also define and store per-sample epidemiological metadata alongside sequencing data, enabling epidemiology analyses. Genome Detective also supports virus-specific analyses when required. Leveraging expert knowledge, we developed and integrated a ToBRFV subtyping tool within the platform, enabling the identification of specific variants. This flexibility allows tailored solutions to be implemented efficiently, ensuring that consortium members can access advanced analyses without the need to set up their own bioinformatics infrastructure. In conclusion, Genome Detective offers a comprehensive and scalable solution for managing and analyzing sequencing data, facilitating collaboration and enhancing our understanding of plant virus epidemics.