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 in the EU and EEA.


In Spain, there are different difficulties that hampers the implementation of the WGS:

1. The lack of personnel makes it very difficult to consolidate the sequencing in a lasting way over time. The staff that currently is dedicated to sequencing belonging to the specific staff at Microbiology Departments. Microbiologists who previously carried out their work in the Microbiology Services are relocated for doing the genome sequence of SARS-CoV-2. The main problem is related with the activity that this staff carried out prior to the pandemia, which has not been covered completely. The 89% of the laboratories present this deficit as a major limiting factor for achieving the objectives set at the national level and Europe of 5-10% of positive samples. The 63% of the network members need hiring laboratory and 1T technicians and 54% bioinformaticians.

2. Currently, the resources used for genomic sequencing have been developed mainly in human genetícs units, which in many hospitals are widely implemented. In general, in Spain there is a deficit in the resources dedicated to sequencing of pathogens detected in clinical samples to investigate infectious diseases in Microbiology Departments do not have this type of resources and development. With exception of AIDS and Hepatitis, adaptation to microbiology is a need. Genomic surveillance of pathogens is a general need throughout the country. The provision of new infrastructure and equipment enhance the implementation of WGS especially in regions that need further development. There are also inequalities among CCAA and within laboratories of the network.

3. The coordination of the network at the national leve! by ISCIII is needed to facilitate the achievement of the ECDC objectives. It has been shown that the existing resources must partially cover the sequencing needs. Now, it is being carried out unevenly between CCAA. An increase in staff related with different processes defined in the 3 phases of this action, may cover immediate needs, at least during the application period. The acquisition of infrastructure will increase the demand for genome sequencing in CCAA that, until now, have not implemented this type of processes. Additionally, the specific mutation detection kits, can quickly become obsolete, will be gradually replaced by genomic sequence systems. Coordination of sequencing activities at the national leve! increases the knowledge of the variants in different geographic regions and allows establishing procedures with a similar yield of results among regions, but also to facilitate comparisons with other EU countries.

Objetivos y Resultados

The general objective of the action is to enhance and/or improve national public health WGS and/or RTPCR capacity. The activities may target public health laboratories at national, regional and/or local level, and should facilitate integration of genomics and these advanced laboratory methods into disease surveillance and outbreak preparedness and response. Results should be directed, tailored towards and contributing towards the following expected outcomes:

• In the short-term, contribution to the establishment of a sustainable, efficient and high capacity WGS and/or RT-PCR infrastructure far national public health microbiology.
• In the short/medium-term, contribution to early detection and enhanced monitoring of emergent and known SARS-CoV-2 variants at the national and the EU/EEA levels.
• In the medium/long-term, contribution to enhanced genomic based infectious disease outbreak investigation capacities at regional, national and/or EU/EEA levels;
• In the medium/long-term, contribution to enhanced routine genomic-based surveillance of infectious diseases at the regional, national and/or EU/EEA levels, in accordance with the "ECDC strategic framework for the integration of molecular and genomic typing into European surveillance and multi-country outbreak investigations"; and
• In the long-term, contribution to enhanced preparedness to timely and efficiently address cross-border outbreaks of infectious diseases and pandemics in the future.

O1: To establish WGS capacity in regional public health laboratories with few experiences in routine sequencing.
O2: To increase the WGS capacity in regional public health laboratories that are sequencing a limited number of samples weekly.
O3: Evaluation of reagents and consumables to improve the process of sequencing and increase of the number of clinical samples sequenced with a good quality.
O4: To hired staff in 32 laboratories at regional and at national level ISCIII.
O5: At National level ISCIII coordination of severa! tasks for improving the technical capacity of regional laboratories.
O6: At national level ISCill, to develop a national SARS-CoV-2 data hub for centralizing genome sequences analysis.

IIS Aragón is working, together with the ISCIII, in the Hospital network through the Hospital Clínico Universitario Lozano Blesa and the Hospital Universitario Miguel Servet.

IP IIS Aragón

Rafael Benito Ruesca (Laboratorio de referencia del HCULB)
Antonio Rezusta y Ana Milagro (Laboratorio de referencia del HUMS)

Organismo Financiador

The HERA INCUBATOR network has received funding from the European Commission (from the European Centre for Disease Prevention and Control under grant agreement no. ECDC/HERA/2021/024).

Total budget: 5.484.986,04 €


Instituto de Salud Carlos III (ISCIII)


23 entidades españolas van como entidades afiliadas del ISCIII, entre las que se encuentra el IIS Aragón.


03/09/2021 - 30/09/2022 (13 meses)