SLOSEQ

Three independent entities that are already partners in HERA 2021 will continue to participate in this grant proposal: NLZOH (National Public Health Laboratory), UL-IMI (Diagnostic and Academic Laboratory) and NIJZ (National Institute of Public Health). In line with the expectation of the call and the general objective of the EU4Health program to protect people in the EU from serious cross-border threats (EU Regulation 2021/522) and national needs, we will continue to expand the project started under HERA 2021. We intend to develop further research of the established RT-PCR infrastructure and WGS. The required objectives will be realized in the technical/scientific part of the project.

Phases of the project and their implementation:

The work will be conducted in 8 work packages (WP).

WP 1 – Coordination and management of the project, which ensures coordination of partners and scientific and effective administrative management of the project. This will ensure that all actions are carried out in accordance with legal, ethical, financial and administrative rules and regulations. We will ensure control over all contractual obligations, which are carried out within the defined budget and according to the highest quality standards. Providing overall support to DP managers and assisting in the preparation of progress reports.

WP 2 – High-throughput detection of SARS-CoV-2, monitoring and detection of known and emerging new variants of SARS-CoV-2 will be a joint work program of NLZOH and UL-IMI; it will aim to further increase RT-PCR capabilities for the detection of SARS-CoV-2, continue national real-time surveillance and expand research to samples from individuals infected with SARS-CoV-2 after (full) vaccination against Covid-19;

WP 3 – This package will contribute to enhanced genomic surveillance of additional pathogens and the inclusion of WGS for selected pathogens in routine public health activities;

WP 4 – We will consolidate data analysis and enable high-quality results by developing pathogen-specific workflows and combining them in user-friendly open source software. Preparation and design of simplified software for the analysis and processing of genome sequencing data. Implementation of software in laboratories for the processing of genome sequencing data;

WP 5 – We will evaluate existing digital dataflows related to genomic monitoring of the SARS-CoV-2 virus and enhance the tools used for field interventions. This will enable rapid and effective response and in-depth monitoring of virus variants that require additional public health measures.

WP 6 – Communicating and disseminating research results in DPs among the target public. Communicating the results of the project with the scientific community, policy makers about the results and impact of the project and Communicating with the general public about the results and impact of the project;

WP 7 – This work package is based on the assessment of the scientific and administrative part of the campaign, the assessment of the ethical framework, the assessment of the risk management plan and the final audit assessment.

WP 8 – This package will ensure the sustainability of the project by: establishing the consolidation of cost-effective WGS surveillance and research, optimizing the logistics of sample collection and archiving, and a long-term WGS pathogen control plan in collaboration with NIJZ.

Added Value

In accordance with the general objectives of this tender, we will ensure: better preparedness and response to threats to public health, sustainability of the microbiological system of public health, a shortcut to the goals of eHealth, rapid reporting of microbiological agents in the patient file and in the e-based health system, progress towards a common European space of health data, progress in the implementation of the European single health Action plan against antimicrobial resistance, maintaining and strengthening genomic surveillance and epidemic response capacity in Slovenia and data exchange in various public domains

Expected Results and Material

To pool expertise in the detection and enhanced surveillance of emerging and known variants of SARS-CoV-2. Upgrading ECDC’s national eHealth and reporting system so that the existing genomic surveillance data pipeline and tools used to collect SARS-CoV-2 surveillance data will be implemented with automated surveillance notifications, while providing an environment for epidemiological investigation, data collection, and contact tracing for response teams. Recording and preparation of data analysis, which will enable high-quality observation of all stakeholders to further improve response time. In-depth programming knowledge to build software. Provide a sustainable plan for further implementation and wider use of the developed system.

Project Duration: 1st of July 2023 – 30th of June 2025.

Supporting Organisation: National Laboratory for Health, Environment and Food (NLZOH)

Project partners: University of Ljubljana (UL) and National Institute of Public Health (NIJZ)

Funding: The project is co-financed with EU funds through the EU4Health program within the LOSframework of the Cooperation Agreement, no. 101112671.

Disclaimer:

Funded by the European Union. The views and opinions expressed are those of the authors and do not necessarily reflect the views and opinions of the European Union or the European Health and Digital Executive Agency (HaDEA). Neither the European Union nor the body that co-finances the campaign can be held responsible for them.