HERA-Incubator

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.