Consolidation and Integration of Whole Genome Sequencing (WGS) into Routine Surveillance in Slovenia

ended

In this grant proposal, three independent entities, already partners in HERA 2021, will continue to collaborate: NLZOH (national public health laboratory), UL-IMI (diagnostic/academic laboratory), and NIJZ (national public health institute). In line with the Call expectations, the EU4Health Programme´s general objective to protect the people of the EU from serious cross-border threats (EU Regulation 2021/522), and national needs, we will continue to expand the HERA 2021 project. We intend to develop further research on the established RT-PCR and WGS infrastructure. The Call objectives will be implemented in the technical/scientific part of the project; in WP 2 we will continue real-time national surveillance of SARS-CoV-2 and detection of known and new SARS-CoV-2 variants. WP 3 will contribute to enhanced genomic surveillance of additional pathogens and integration of WGS for selected pathogens into routine public health activities. We will consolidate data analysis and enable high-quality results by development of pathogen-specific workflows, combining them in user-friendly open-source software and Singularity based pipelines (WP 4). Detailed descriptions of the NCC-AMR's organisation, tasks, and responsibilities will be prepared (WP 5). In WP 6, we will upgrade the existing genomic surveillance data pipelines and tools used for collecting SARS-CoV-2 surveillance data. In line with the general objectives of this call, we will ensure: better preparedness and response to public health threats, sustainability of the public health microbiology system, shortcut to eHealth goals, rapid reporting of microbiological agents to patient's record and in e-based heath-system, progress towards common European Health Data Space, progress in implementing the European One Health Action Plan against Antimicrobial Resistance, maintain and strengthen genomic surveillance and epidemic response capacities in Slovenia and data sharing across various public domains.