Enhancing SARS-CoV-2 Surveillance through Regular Genomic Sequencing in Spain: The RELECOV Network

Area of Science:

• Virology
• Genomics
• Public Health

Background:

• Millions of SARS-CoV-2 whole genome sequences exist, but robust surveillance requires quality data and systems.
• The Spanish network for coronavirus laboratories (RELECOV) was established to accelerate SARS-CoV-2 detection, analysis, and evaluation nationally.
• A European Centre for Disease Prevention and Control (ECDC)-HERA-Incubator action partially funded RELECOV.

Purpose of the Study:

• To evaluate the technical capacity of the RELECOV network through a SARS-CoV-2 sequencing quality control assessment (QCA).
• To monitor SARS-CoV-2 using genomic data from 48,578 viral genomes.
• To assess the impact of RELECOV network actions on viral sequence sharing and genomic surveillance.

Main Methods:

• Development and implementation of a SARS-CoV-2 sequencing quality control assessment (QCA).
• Analysis of 48,578 SARS-CoV-2 viral genomes.
• Phylogenetic analyses to correlate genomic data with variant clusters.
• Identification of lineage/sublineage-defining mutations for variant tracking.

Main Results:

• The QCA showed a lower hit rate for lineage assignment compared to variant assignment.
• RELECOV network actions resulted in a 36% increase in viral sequence sharing.
• Distinct mutation profiles were identified for Delta and Omicron variants.
• Phylogenetic analyses confirmed variant clusters and established a robust reference tree.

Conclusions:

• The RELECOV network significantly improved SARS-CoV-2 genomic surveillance in Spain.
• The network provided and evaluated genomic tools for efficient viral genome monitoring and characterization.
• RELECOV enhances knowledge dissemination and promotes robust genomic surveillance of SARS-CoV-2.