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Using a Pan-Viral Microarray Assay Virochip to Screen Clinical Samples for Viral Pathogens
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A Genomic Surveillance Circuit for Emerging Viral Pathogens.

Carlos S Casimiro-Soriguer1,2, Maria Lara1, Andrea Aguado1

  • 1Platform of Computational Medicine, Andalusian Public Foundation Progress and Health-FPS, 41013 Sevilla, Spain.

Microorganisms
|April 26, 2025
PubMed
Summary

Genomic surveillance in Andalusia sequenced over 42,500 SARS-CoV-2 genomes, tracking variants like Omicron. This regional circuit enhances epidemic preparedness and public health decision-making.

Keywords:
COVID-19SARS-CoV-2genomic surveillancewhole-genome sequencing (WGS)

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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.