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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.
Details
Public health;
Surveillance;
Phylogenetics;
Epidemiology;
Genomics;
Severe acute respiratory syndrome coronavirus 2;
Mutation;
Bioinformatics;
Data processing;
Genomes;
Viral diseases;
COVID-19;
Pathogens;
Data analysis;
Electronic health records;
Pandemics;
Epidemics;
Hospitals;
Sequences;
Decision making;
Health risks;
Disease transmission;
Evolution
; Lara, Maria 2
; Aguado, Andrea 2
; Loucera Carlos 1
; Ortuño, Francisco M 3
; Lorusso, Nicola 4 ; Navarro-Marí, Jose M 5
; Sanbonmatsu-Gámez Sara 5
; Camacho-Martinez, Pedro 6 ; Merino-Diaz, Laura 6 ; de Salazar Adolfo 7
; Fuentes, Ana 7
; Lepe, Jose A 8
; García Federico 7
; Dopazo Joaquín 1
; Perez-Florido, Javier 1
1 Platform of Computational Medicine, Andalusian Public Foundation Progress and Health-FPS, 41013 Sevilla, Spain, Institute of Biomedicine of Seville (IBiS), University Hospital Virgen del Rocío/CSIC/University of Seville, 41013 Sevilla, Spain; [email protected]
2 Platform of Computational Medicine, Andalusian Public Foundation Progress and Health-FPS, 41013 Sevilla, Spain
3 Platform of Computational Medicine, Andalusian Public Foundation Progress and Health-FPS, 41013 Sevilla, Spain, Department of Computer Engineering, Automatics and Robotics, University of Granada, 18071 Granada, Spain
4 Dirección General de Salud Pública, Consejería de Salud y Consumo, Junta de Andalucía, 41020 Sevilla, Spain
5 Servicio de Microbiología, Hospital Virgen de las Nieves, 18014 Granada, Spain, Instituto de Investigación Biosanitaria ibs.GRANADA, 18012 Granada, [email protected] (F.G.)
6 Servicio de Microbiología, Unidad Clínica Enfermedades Infecciosas, Microbiología y Medicina Preventiva, Hospital Universitario Virgen del Rocío, 41013 Sevilla, Spain
7 Instituto de Investigación Biosanitaria ibs.GRANADA, 18012 Granada, [email protected] (F.G.), Servicio de Microbiología, Hospital Universitario San Cecilio, 18016 Granada, Spain, Centro de Investigación Biomédica en Red en Enfermedades Infecciosas (CIBERINFEC), Instituto de Salud Carlos III (ISCIII), 28029 Madrid, Spain
8 Institute of Biomedicine of Seville (IBiS), University Hospital Virgen del Rocío/CSIC/University of Seville, 41013 Sevilla, Spain; [email protected], Servicio de Microbiología, Unidad Clínica Enfermedades Infecciosas, Microbiología y Medicina Preventiva, Hospital Universitario Virgen del Rocío, 41013 Sevilla, Spain, Centro de Investigación Biomédica en Red en Enfermedades Infecciosas (CIBERINFEC), Instituto de Salud Carlos III (ISCIII), 28029 Madrid, Spain