ECDC supports EU/EEA Member States in rapid detection of SARS-CoV-2 variants

News story

ECDC and the European Commission’s Directorate-General for Health and Food Safety (DG SANTE) have launched a number of activities to help strengthen EU/EEA Member States’ capacity for detection of SARS-CoV-2 variants in the shorter and longer term. These activities are one of five action areas of the ‘HERA Incubator’, a new EU bio-defence preparedness plan against SARS-CoV-2 variants launched by the European Commission on 17 February 2021.

“As we continue to fight the COVID-19 pandemic, new challenges and threats emerge, such as variants which challenge vaccine effectiveness. These have the potential to complicate our sustained and united efforts to overcome the virus,” says Andrea Ammon, ECDC Director. “This very real threat of variants requires determined, collective, and immediate action. ECDC will work closely with the HERA Incubator to ensure that Member States have sufficient sequencing capacities and access to sequencing support services.”

Outsourced support to EU/EEA Member States and neighbouring countries for whole genome sequencing

Whole genome sequencing (WGS) maps out the unique genetic blueprints of different strains of the virus, and, as such, it is an essential tool for making informed public health decisions. It is the key to identifying variants, as well as monitoring their spread in communities and populations. The WGS services under the HERA Incubator include shipping of samples, laboratory sample preparation, sequencing and basic sequence analysis support. This will guarantee the sequencing of up to 6 000 isolates per week per country. In 2021, ECDC and the European Commission have made available EUR 27 000 000 for outsourced WGS services.

National WGS and/or RT-PCR infrastructure support programme for EU/EEA public health authorities

A sizeable and coordinated infrastructure investment in public health laboratories will allow Member States to develop a significant and cost-effective SARS-CoV-2 variant screening system. The aim of the initiative is not only to provide capacity for the next phase of the COVID-19 pandemic, but also to set up a sustainable infrastructure that can be used more broadly, in line with national and EU-level strategies. Investments into all the essential areas of the workflow for WGS and RT-PCR (a laboratory method for detecting the presence of specific genetic material in any pathogen, including a virus) could be included in projects under this programme, if this can be justified by the implementing country. Examples include laboratory sample management systems and software and data analysis tools. The total budget for the co-financing of the successful applications selected under the national WGS and/or RT-PCR infrastructure support programme is EUR 83 000 000.

Cross-border capacity-building support programme

Training and other capacity-building activities are essential for the infrastructure investments in order to ensure that they become sustainably integrated into national public health frameworks for routine use. The plan is that these activities, which are still under development, will include centralised support for national and regional public health laboratories to develop WGS competencies in the longer-term perspective. In 2021, EUR 2 000 000 has been set aside for such support activities.



As part of the EU Health Union proposals of 11 November 2020, the European Commission plans to set up the EU Health Emergency Preparedness and Response Authority (HERA).

HERA’s mission will be to enable the EU/EEA Member States to rapidly deploy the most advanced medical countermeasures, to ensure capacity and readiness to respond to cross-border threats and emergencies – whether natural or deliberate.

This new body will complement and create synergies with the work of existing EU agencies, in particular ECDC and the European Medicines Agency (EMA). The European Commission is planning to put forward a legislative proposal for HERA in September 2021.

The HERA Incubator is one of several preparatory actions that will serve as a blueprint for the EU's long-term preparedness for health emergencies, and will pilot some of the aspects that may be covered by the new authority. The HERA Incubator focuses on five specific action areas:

  1. Rapid detection of SARS-CoV-2 variants (as described in the article above)
  2. Swift adaptation of COVID-19 vaccines (investments in research and innovation)
  3. Setting up a European clinical trials network (VACCELERATE)
  4. Fast-tracking the regulatory approval process
  5. Ramping up industrial production of COVID-19 vaccines against variants of concern.