A Genomic Surveillance Circuit for Emerging Viral Pathogens

Area of Science:

• Public Health
• Genomics
• Epidemiology

Background:

• Genomic surveillance is vital for tracking viral evolution and spread.
• Effective SARS-CoV-2 monitoring requires coordinated regional efforts.
• Decentralized healthcare systems present unique challenges for large-scale sequencing.

Purpose of the Study:

• To establish and evaluate a regional genomic surveillance circuit for SARS-CoV-2 in Andalusia, Spain.
• To systematically sequence and analyze viral genomes to understand variant dynamics.
• To integrate genomic data with epidemiological information for public health action.

Main Methods:

• Established a network of 27 hospitals for sample collection.
• Utilized three reference laboratories for viral genome sequencing.
• Centralized data analysis and reporting via a bioinformatics platform.
• Sequenced over 42,500 SARS-CoV-2 genomes between 2021 and 2025.

Main Results:

• Successfully identified and tracked major SARS-CoV-2 variants, including Alpha, Delta, and Omicron sublineages.
• Monitored the evolutionary dynamics and transition between successive viral waves.
• Demonstrated the feasibility of large-scale genomic surveillance within a decentralized healthcare system.

Conclusions:

• The Andalusian genomic surveillance circuit effectively supports variant detection and outbreak investigation.
• Integrated genomic and epidemiological data enhance public health decision-making and epidemic preparedness.
• The framework's expansion to other pathogens highlights its long-term value for infectious disease monitoring.