A Genomic Surveillance Circuit for Emerging Viral Pathogens
Genomic surveillance has been crucial in monitoring the evolution and spread of SARS-CoV-2. In Andalusia (Spain), a coordinated genomic surveillance circuit was established to systematically sequence and analyze viral genomes across the region. This initiative organizes sample collection through 27 hospitals, which act as regional hubs within their respective health districts. Sequencing is performed at three reference laboratories, with downstream data analysis and reporting centralized at a bioinformatics platform. From 2021 to 2025, over 42,500 SARS-CoV-2 genomes were sequenced, enabling the identification of major variants and their evolutionary dynamics. The circuit tracked the transition from Alpha and Delta to successive Omicron waves, including both recombinant and non-recombinant clades. The integration of genomic and epidemiological data facilitated rapid variant detection, outbreak investigation, and public health decision making. This surveillance framework at a regional granularity demonstrates the feasibility of large-scale sequencing within a decentralized healthcare system and has expanded to monitor other pathogens, reinforcing its value for epidemic preparedness. Continued investment in genomic surveillance is critical for tracking viral evolution, guiding interventions, and mitigating future public health threats.
Authors
- Carlos Loucera (ORCID: https://orcid.org/0000-0001-9598-6965)
- Adolfo de Salazar (ORCID: https://orcid.org/0000-0002-4318-858X)
- Féderico García (ORCID: https://orcid.org/0000-0001-7611-781X)
- Ana Fuentes (ORCID: https://orcid.org/0000-0002-2057-2730)
- Francisco Ortuño (ORCID: https://orcid.org/0000-0001-7424-1753)
- Javier Pérez-Florido (ORCID: https://orcid.org/0000-0002-0223-9889)
- José María Navarro‐Marí (ORCID: https://orcid.org/0000-0002-5227-5167)
- Laura Merino-Díaz
- Joaquı́n Dopazo (ORCID: https://orcid.org/0000-0003-3318-120X)
- Sara Sanbonmatsu‐Gámez (ORCID: https://orcid.org/0000-0003-1859-927X)
- José Antonio Lepe (ORCID: https://orcid.org/0000-0002-3635-4930)
- Pedro Camacho‐Martínez (ORCID: https://orcid.org/0000-0002-6331-4600)
- Carlos S. Casimiro‐Soriguer (ORCID: https://orcid.org/0000-0003-1774-2580)
- Andrea Aguado (ORCID: https://orcid.org/0009-0008-0515-6510)
- Nicola Lorusso (ORCID: https://orcid.org/0000-0003-2829-2546)
- María Pía Lara (ORCID: https://orcid.org/0000-0001-6802-6424)
Institutions
- Universidad de Granada (ES)
- Instituto de Salud Carlos III (ES)
- Fundación Progreso y Salud (ES)
- Instituto de Investigación Biosanitaria de Granada (ES)
- Centro de Investigación Biomédica en Red (ES)
- Hospital Universitario Virgen de las Nieves (ES)
- Instituto de Biomedicina de Sevilla (ES)
- Hospital Universitario Virgen del Rocío (ES)
- Universidad de Sevilla (ES)
- Junta de Andalucía (ES)
Publication Details
- Journal
- Microorganisms
- Published
- 2025-04-16
- DOI
- https://doi.org/10.3390/microorganisms13040912
- Citations
- 2
- Primary Topic
- SARS-CoV-2 and COVID-19 Research
- Type
- article
- Field-Weighted Citation Impact
- 2.79
Funders
- European Commission
- European Centre for Disease Prevention and Control
- Consejería de Salud y Familias, Junta de Andalucía
- Junta de Andalucía
- Horizon 2020 Framework Programme
- Instituto de Salud Carlos III
- European Regional Development Fund