Consolidation of genome sequencing and infrastructure processes for infectious disease surveillance and outbreak detection

Consolidation of WGS/RT-PCR activities in the countries that have received support in 2021, with the aim of ensuring the sustainable use and integration of the improved infrastructure into routine surveillance and disease bridge testing, in synergy with relevant ongoing work at international level.

Project description

In this follow up project, the consolidation of WGS/RT-PCR activities aiming to ensure the sustainable use and integration of enhanced infrastructure into routine surveillance and outbreak investigation activities, in synergy with relevant ongoing work at international level, is key priority. Identified challenges and mid-term aims were identified and will contribute together with the involvement of relevant and high-level stakeholders to a better workflow, enhanced capacity and sustainable and manageable use of the provided infrastructure on the long run. Key agencies in the countries Austria, Croatia, Greece and Hungary are working together to achieve these common goals. The partners are AGES (AUT), CIPH (HR), EODY (GR) and NCPHP (HU).

In the course of the previous project round, the focus on national infrastructure and capacity up-scaling enhancing whole genome sequencing (WGS) and/or reverse transcription polymerase chain reaction (RT-PCR) to respond to the COVID-19 pandemic and future health threats (HERA) set a solid but challenging basis for the enhancement of processes in national Health Agencies and public analytic facilities.
Now, the focus will lie on the joint continuation of automation/optimization/validation of WGS/RT-PCR capacities (laboratory, bioinformatics, IT) and establishment and validation of new genome sequencing methods (laboratory and bioinformatics) and on the distribution of knowledge among the consortium members and other relevant stakeholders.


  • Establishing a sustainable, efficient and high-performing WGS and/or RT-PCR infrastructure for the expansion of microbiology in the national health care system
  • Improved routine genome-based surveillance of infectious diseases at regional, national and EU/EEA levels in accordance with strategic frameworks
  • Increased genome-based investigations of infectious disease outbreaks and build infrastructure capacity at regional, national and/or EU/EAA levels
  • Early detection and enhanced surveillance of emerging and known SARS-CoV-2 variants at national and EU/EAA levels
  • Improved preparedness for timely and cross-border detection of infectious disease outbreaks and pandemics in the future

Project Profile

Together with the consortium partners Greece (EODY), Croatia (CIPH) and Hungary (NCPHP), AGES as coordinator was awarded the Joint Action in the EU4Health program HERA 2 - Consolidation of WGS/RT-PCR and infrastructure processes in outbreak surveillance and investigation in autumn 2022. A total budget of € 4.54 million is foreseen for this project.

Project details Description
Project Actronym: HERA 2
Project Management: AGES
Project partners: CIPH (HR), EODY (GR), NCPHP (HU).
Funding: European Health and Digital Executive Agency (HaDEA) under the EU4Health Program
Project duration 10.2022 until 03.2026




Last updated: 13.05.2024

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