A Genomic Surveillance Circuit for Emerging Viral Pathogens

The SARS-CoV-2 whole-genome sequences described in this study are available in the European Nucleotide Archive (ENA) under the identifier PRJEB44396 and in GISAID.

Detalles Bibliográficos
Autores: Casimiro-Soriguer, Carlos S., Lara, Maria, Aguado, Andrea, Loucera, Carlos, Ortuño, Francisco M., Lorusso, Nicola, Navarro-Marí, Jose M., Sanbonmatsu-Gámez, Sara, Camacho-Martinez, Pedro, Merino-Diaz, Laura, de Salazar, Adolfo, Fuentes, Ana, The Andalusian Covid-Sequencing Initiative, Lepe, Jose A., García, Federico, Dopazo, Joaquín, Perez-Florido, Javier
Tipo de recurso: artículo
Estado:Versión publicada
Fecha de publicación:2025
País:España
Institución:Consejo Superior de Investigaciones Científicas (CSIC)
Repositorio:DIGITAL.CSIC. Repositorio Institucional del CSIC
OAI Identifier:oai:digital.csic.es:10261/390184
Acceso en línea:http://hdl.handle.net/10261/390184
https://api.elsevier.com/content/abstract/scopus_id/105003727039
Access Level:acceso abierto
Palabra clave:COVID-19
SARS-CoV-2
Genomic surveillance
Whole-genome sequencing (WGS)
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spelling A Genomic Surveillance Circuit for Emerging Viral PathogensCasimiro-Soriguer, Carlos S.Lara, MariaAguado, AndreaLoucera, CarlosOrtuño, Francisco M.Lorusso, NicolaNavarro-Marí, Jose M.Sanbonmatsu-Gámez, SaraCamacho-Martinez, PedroMerino-Diaz, Laurade Salazar, AdolfoFuentes, AnaThe Andalusian Covid-Sequencing InitiativeLepe, Jose A.García, FedericoDopazo, JoaquínPerez-Florido, JavierCOVID-19SARS-CoV-2Genomic surveillanceWhole-genome sequencing (WGS)The SARS-CoV-2 whole-genome sequences described in this study are available in the European Nucleotide Archive (ENA) under the identifier PRJEB44396 and in GISAID.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.This study has been funded by the European Union’s EU4Health programme (EU4HEALTH-101113109), and the HERA incubator plan (ECDC/HERA/2021/024 ECD.12241). J.D. has been supported by grant PT17/0009/0006 from the ISCIII, co-funded by the European Regional Development Fund (ERDF), as well as the European Commission’s H2020 ELIXIR-EXCELERATE (Grant Agreement No. 676559) and by the Consejería de Salud y Familias-Junta de Andalucía (COVID-0012-2020).Peer reviewedMultidisciplinary Digital Publishing InstituteEuropean CommissionInstituto de Salud Carlos IIIJunta de AndalucíaCasimiro-Soriguer, Carlos S. [0000-0003-1774-2580]Consejo Superior de Investigaciones Científicas [https://ror.org/02gfc7t72]202520252025info:eu-repo/semantics/articlehttp://purl.org/coar/resource_type/c_6501Publisher's versioninfo:eu-repo/semantics/publishedVersionapplication/pdfhttp://hdl.handle.net/10261/390184https://api.elsevier.com/content/abstract/scopus_id/105003727039reponame:DIGITAL.CSIC. Repositorio Institucional del CSICinstname:Consejo Superior de Investigaciones Científicas (CSIC)Inglés#PLACEHOLDER_PARENT_METADATA_VALUE#info:eu-repo/grantAgreement/EC/H2020/676559The underlying dataset has been published as supplementary material of the article in the publisher platform at DOI https://doi.org/10.3390/microorganisms13040912https://doi.org/10.3390/microorganisms13040912Síinfo:eu-repo/semantics/openAccessoai:digital.csic.es:10261/3901842026-05-22T06:33:51Z
dc.title.none.fl_str_mv A Genomic Surveillance Circuit for Emerging Viral Pathogens
title A Genomic Surveillance Circuit for Emerging Viral Pathogens
spellingShingle A Genomic Surveillance Circuit for Emerging Viral Pathogens
Casimiro-Soriguer, Carlos S.
COVID-19
SARS-CoV-2
Genomic surveillance
Whole-genome sequencing (WGS)
title_short A Genomic Surveillance Circuit for Emerging Viral Pathogens
title_full A Genomic Surveillance Circuit for Emerging Viral Pathogens
title_fullStr A Genomic Surveillance Circuit for Emerging Viral Pathogens
title_full_unstemmed A Genomic Surveillance Circuit for Emerging Viral Pathogens
title_sort A Genomic Surveillance Circuit for Emerging Viral Pathogens
dc.creator.none.fl_str_mv Casimiro-Soriguer, Carlos S.
Lara, Maria
Aguado, Andrea
Loucera, Carlos
Ortuño, Francisco M.
Lorusso, Nicola
Navarro-Marí, Jose M.
Sanbonmatsu-Gámez, Sara
Camacho-Martinez, Pedro
Merino-Diaz, Laura
de Salazar, Adolfo
Fuentes, Ana
The Andalusian Covid-Sequencing Initiative
Lepe, Jose A.
García, Federico
Dopazo, Joaquín
Perez-Florido, Javier
author Casimiro-Soriguer, Carlos S.
author_facet Casimiro-Soriguer, Carlos S.
Lara, Maria
Aguado, Andrea
Loucera, Carlos
Ortuño, Francisco M.
Lorusso, Nicola
Navarro-Marí, Jose M.
Sanbonmatsu-Gámez, Sara
Camacho-Martinez, Pedro
Merino-Diaz, Laura
de Salazar, Adolfo
Fuentes, Ana
The Andalusian Covid-Sequencing Initiative
Lepe, Jose A.
García, Federico
Dopazo, Joaquín
Perez-Florido, Javier
author_role author
author2 Lara, Maria
Aguado, Andrea
Loucera, Carlos
Ortuño, Francisco M.
Lorusso, Nicola
Navarro-Marí, Jose M.
Sanbonmatsu-Gámez, Sara
Camacho-Martinez, Pedro
Merino-Diaz, Laura
de Salazar, Adolfo
Fuentes, Ana
The Andalusian Covid-Sequencing Initiative
Lepe, Jose A.
García, Federico
Dopazo, Joaquín
Perez-Florido, Javier
author2_role author
author
author
author
author
author
author
author
author
author
author
author
author
author
author
author
dc.contributor.none.fl_str_mv European Commission
Instituto de Salud Carlos III
Junta de Andalucía
Casimiro-Soriguer, Carlos S. [0000-0003-1774-2580]
Consejo Superior de Investigaciones Científicas [https://ror.org/02gfc7t72]
dc.subject.none.fl_str_mv COVID-19
SARS-CoV-2
Genomic surveillance
Whole-genome sequencing (WGS)
topic COVID-19
SARS-CoV-2
Genomic surveillance
Whole-genome sequencing (WGS)
description The SARS-CoV-2 whole-genome sequences described in this study are available in the European Nucleotide Archive (ENA) under the identifier PRJEB44396 and in GISAID.
publishDate 2025
dc.date.none.fl_str_mv 2025
2025
2025
dc.type.none.fl_str_mv info:eu-repo/semantics/article
http://purl.org/coar/resource_type/c_6501
Publisher's version
info:eu-repo/semantics/publishedVersion
format article
status_str publishedVersion
dc.identifier.none.fl_str_mv http://hdl.handle.net/10261/390184
https://api.elsevier.com/content/abstract/scopus_id/105003727039
url http://hdl.handle.net/10261/390184
https://api.elsevier.com/content/abstract/scopus_id/105003727039
dc.language.none.fl_str_mv Inglés
language_invalid_str_mv Inglés
dc.relation.none.fl_str_mv #PLACEHOLDER_PARENT_METADATA_VALUE#
info:eu-repo/grantAgreement/EC/H2020/676559
The underlying dataset has been published as supplementary material of the article in the publisher platform at DOI https://doi.org/10.3390/microorganisms13040912
https://doi.org/10.3390/microorganisms13040912
Sí
dc.rights.none.fl_str_mv info:eu-repo/semantics/openAccess
eu_rights_str_mv openAccess
dc.format.none.fl_str_mv application/pdf
dc.publisher.none.fl_str_mv Multidisciplinary Digital Publishing Institute
publisher.none.fl_str_mv Multidisciplinary Digital Publishing Institute
dc.source.none.fl_str_mv reponame:DIGITAL.CSIC. Repositorio Institucional del CSIC
instname:Consejo Superior de Investigaciones Científicas (CSIC)
instname_str Consejo Superior de Investigaciones Científicas (CSIC)
reponame_str DIGITAL.CSIC. Repositorio Institucional del CSIC
collection DIGITAL.CSIC. Repositorio Institucional del CSIC
repository.name.fl_str_mv
repository.mail.fl_str_mv
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score 15,812429

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