Strengthened capacity and Sustainable Infrastructures for Sequencing-based diagnostic preparedness

Statens Serum Institut (SSI) is the national public health institute under the Ministry of Health and works to prevent and fight infectious diseases and congenital diseases through research, monitoring, diagnostics, and advice. During the SARS-CoV-2 pandemic SSI was the primary coordinator of the national SARS-CoV-2 response and WGS capacities both at SSI and at the Departments of Clinical Microbiology (DCM) in the five regions of Denmark was increased substantially. However, the SARS-CoV-2 workflow and infrastructure was developed during the fluctuating epidemic and is not directly applicable to other pathogens of interest. SSI will therefore, based on thorough dialogue with external national and international stakeholders, work to fulfill the three primary needs identified. One need is to optimise and further develop surveillance-related pipelines and workflows to secure that WGS data for surveillance is of comparable quality. A second need is to develop IT infrastructures and bioinformatics tools that allows for sharing WGS data and analysis results in as real-time as possible. A third need is to develop common Standard Operation Procedures (SOPs) for producing, analyzing and sharing of WGS data. In order for the generated WGS surveillance data to become data-for-action it is important that the combination of other laboratory data, epidemiological data, and WGS data are built into the supporting IT infrastructure. This will be addressed in all relevant work packages. SSI is committed to making data open and transparent where possible as we have carried out with our extensive sharing of data for SARS-CoV-2 to GISAID and ENA. This process is conducted for some of our other pathogen species but not all. We want to ensure we continue to disseminate information to National, EU and global institutes in a timely and understandable manner. Throughout the project, sustainability will be on the agenda.