Project HERA 2

Project HERA 2

Project number: 101113387

Project name: Genomic surveillance of selected infectious diseases in the Czech Republic

Project acronym: HERA2CZ

Call: EU4H-2022-DGA-MS-IBA-1

The Name of the Call: Direct grants to Member States’ authorities: Enhancing whole genome sequencing (WGS) and/or reverse transcription polymerase chain reaction (RT-PCR) national infrastructures and capacities to respond to the COVID-19 pandemic and future health threats

Topic: EU4H-2022-DGA-MS-IBA-01-02

Topic Name: Consolidation of WGS and RT-PCR activities in countries that received support in 2021 aiming to ensure the sustainable use and integration of enhanced infrastructure into routine surveillance and outbreak investigation activities, in synergy with relevant on-going work at international level.

Type of action: EU4H-PJG

Project start: 1/10/2022

Project end: 30/6/2025

Project Duration: 33 months

Funding: The European Health and Digital Executive Agency (HADEA)

Grant: 1 393 630 EUR

Beneficiary: National Institute of Public Health

Partners/Affiliated Entities: none


Project Goals:

The project aims to improve the capacity of National Reference Laboratories (NRLs) in the National Institute of Public Health (NIPH) in Prague for genotypic characterization of a range of human pathogens (especially SARS-CoV-2 and other respiratory viruses, bacterial pathogens with cross-border threat potential, including antibiotic-resistant bacteria) with public health significance. The whole genome sequencing (WGS) is currently the state-of-the-art method for detailed characterization of microorganisms, as it provides a complete description of the genetic information of a given microorganism and its objective outputs allow immediate interlaboratory comparisons at the national and international levels.

The aim of the project is to improve the availability of genomic surveillance of communicable diseases in order to identify and characterize specific determinants for the description and identification of clonal lineages with significant potential for their spread. The project responds to the need to ensure genomic surveillance within European structures (specifically the ECDC). Without the implementation of routine genomic surveillance, monitoring and addressing national and cross-border threats of infectious diseases and antibiotic resistance is not possible.

This project directly builds on the previous project granted under ECDC procedure ECDC/HERA/2021/004.ECD.12218. More information about the HERA project.


The project consists of 5 work packages (WP):

  • Leader: Jana Kozáková
  • Project management, evaluation, communication and sustainability –MNGECS. WP’s objective focuses on the effective management, coordination, communication, evaluation, and sustainability of the project. Management efforts prioritize achieving overall project objectives within the budget and timeline, emphasizing coordination of work plans and progress among Work Package leaders and ensuring accurate reporting. Communication strategies include developing a Communication strategy to reach target audiences and raise awareness of key project outcomes. Evaluation processes involve assessing specific project objectives and maintaining high-quality standards for produced data. WP1 also focuses on the sustainability of project results by elaborating on a plan for exploiting enhanced knowledge and infrastructure for improved cooperation in pathogen surveillance.
  • Leader: Helena Jiřincová
  • COVID, RSV, influenza, surveillance – CORINFES. WP’s objective is to enhance Czech capacities in preventing and controlling communicable diseases and facilitate international data and protocol sharing. Aligned with ECDC priorities, WP2 focuses on integrating SARS-CoV-2 surveillance into the national ARI/ILI surveillance system and linking it with WGS data for respiratory or emerging viruses. The Mass Array technology, validated in a previous project (HERA), is adopted for detecting single nucleotide polymorphisms (SNP) associated with influenza virus resistance. We would like to adopt this technology for the detection of SNP that are responsible for the anti-virotic resistance of influenza viruses recently circulating in the human population (A/H1N1, A/H3N2 and B/Yamagata/Victoria).
  • Publications related to WP2
  • Other sources”
    • Information about previous project HERA
  • Leader: Martina Bielaszewska
  • Genomic surveillance and outbreak investigation of bacterial food-borne diseases  – BACFOOD. WP’s objective is to conduct real-time whole genome sequencing of significant bacterial food-borne pathogens. This activity aims to facilitate the continuous surveillance of food- and water-borne diseases (FWD) and prompt early outbreak investigations in the Czech Republic. The approach is designed to significantly enhance protection of the population against both national and cross-border threats posed by FWD pathogens. WP3 has specific objectives, including the strengthening of whole genome sequencing capacity for molecular typing of crucial bacterial food-borne pathogens, such as Salmonella sp. and Shiga toxin-producing E. coli (STEC). The early detection of clusters enables swift investigations of FWD outbreaks, and the identification of genetic determinants associated with antibiotic resistance is an integral part of the strategy in relation to FWD outbreak investigations.
  • Publications related to WP3
  • Other sources:
  • Leader: Jana Kozáková
  • Vaccine Preventable Diseases (invasive meningococcal disease, invasive pneumococcal disease, invasive disease caused by Haemophilus, invasive disease caused by B. pertussis) – VACPREV. WP4’s objective is the implementation of whole genome sequencing (WGS) as a routine practice in National Reference Laboratories (NRLs) responsible for national disease surveillance caused by meningococci, pneumococci, haemophilus, and B. pertussis. The WGS data generated within the project will be reported to the international databases for outbreak investigations, control-oriented surveillance, and strategy-oriented surveillance of invasive diseases caused by the pathogens mentioned. The implementation involves establishing WGS protocols, which include DNA extraction, quality control, sequencing library preparation, and data analysis. The purchase of WGS sequencing equipment within the project will enhance the ability to perform WGS for agents mentioned contributing to improved disease surveillance and control.
  • Publications related to WP4
  • Other sources:
  • Leader: Helena Žemličková
  • Antimicrobial resistance genes surveillance – ATBRES. WP’s objective focuses on implementing whole genome sequencing (WGS) into European surveillance and national/international outbreak investigations, and enhancing diagnostic capabilities to detect carbapenem-resistant and/or colistin-resistant Enterobacterales (CRE/CCRE). The primary objectives include implementing standardized WGS-based genome analysis methods, performing quality control on WGS, identifying genetic determinants associated with antibiotic resistance, and confirming and identifying outbreaks of priority pathogens linked to antimicrobial resistance (AMR). The ultimate goal is to establish a robust methodology for WGS and effective tools for enhanced surveillance of bacteria contributing to the spread of antibiotic resistance.
  • Publications related to WP5
  • Other sources:

Press releases, leaflets, links

Project’s Coordinator: 

Jana Kozáková, MD

00420 267 082 101


Acknowledgement of funding:

Project „Genomic surveillance of selected infectious diseases in the Czech Republic“ (HERA2CZ) was funded by the European Union. Views and opinions expressed are however those of the author(s) only and do not necessarily reflect those of the European Union or the European Health and Digital Executive Agency (HADEA). Neither the European Union nor the European Health and Digital Executive Agency (HADEA) can be held responsible for them.