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Vázquez-Morón S, Iglesias-Caballero M, Lepe JA, Garcia F, Melón S, Marimon JM, García de Viedma D, Folgueira MD, Galán JC, López-Causapé C, Benito-Ruesca R, Alcoba-Florez J, Gonzalez Candelas F, Toro MD, Fajardo M, Ezpeleta C, Lázaro F, Pérez Castro S, Cuesta I, Zaballos A, Pozo F, Casas I. Enhancing SARS-CoV-2 Surveillance through Regular Genomic Sequencing in Spain: The RELECOV Network. Int J Mol Sci 2023; 24:ijms24108573. [PMID: 37239920 DOI: 10.3390/ijms24108573] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2023] [Revised: 04/25/2023] [Accepted: 05/03/2023] [Indexed: 05/28/2023] Open
Abstract
Millions of SARS-CoV-2 whole genome sequences have been generated to date. However, good quality data and adequate surveillance systems are required to contribute to meaningful surveillance in public health. In this context, the network of Spanish laboratories for coronavirus (RELECOV) was created with the main goal of promoting actions to speed up the detection, analyses, and evaluation of SARS-CoV-2 at a national level, partially structured and financed by an ECDC-HERA-Incubator action (ECDC/GRANT/2021/024). A SARS-CoV-2 sequencing quality control assessment (QCA) was developed to evaluate the network's technical capacity. QCA full panel results showed a lower hit rate for lineage assignment compared to that obtained for variants. Genomic data comprising 48,578 viral genomes were studied and evaluated to monitor SARS-CoV-2. The developed network actions showed a 36% increase in sharing viral sequences. In addition, analysis of lineage/sublineage-defining mutations to track the virus showed characteristic mutation profiles for the Delta and Omicron variants. Further, phylogenetic analyses strongly correlated with different variant clusters, obtaining a robust reference tree. The RELECOV network has made it possible to improve and enhance the genomic surveillance of SARS-CoV-2 in Spain. It has provided and evaluated genomic tools for viral genome monitoring and characterization that make it possible to increase knowledge efficiently and quickly, promoting the genomic surveillance of SARS-CoV-2 in Spain.
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Affiliation(s)
- Sonia Vázquez-Morón
- Respiratory Viruses and Influenza Unit, National Centre for Microbiology, Instituto de Salud Carlos III, 28222 Majadahonda, Spain
- CIBER de Epidemiología y Salud Pública (CIBERESP), ISCIII, 28029 Madrid, Spain
| | - María Iglesias-Caballero
- Respiratory Viruses and Influenza Unit, National Centre for Microbiology, Instituto de Salud Carlos III, 28222 Majadahonda, Spain
| | - José Antonio Lepe
- Microbiology Service, Hospital Universitario Virgen del Rocio, 41013 Sevilla, Spain
| | - Federico Garcia
- Microbiology Service, Hospital Universitario San Cecilio, Instituto de Investigación Biosanitaria Ibs. Granada, 18016 Granada, Spain
- CIBER de Enfermedades Infecciosas (CIBERINFEC), ISCIII, 28029 Madrid, Spain
| | - Santiago Melón
- Microbiology Service, Hospital Universitario Central de Asturias, 33011 Oviedo, Spain
| | - José M Marimon
- Microbiology Service, Instituto de Investigación Sanitaria Biodonostia, Hospital Universitario Donostia, 20014 Donostia-San Sebastian, Spain
| | - Darío García de Viedma
- Microbiology Service, Hospital General Universitario Gregorio Marañón, Instituto de Investigación Sanitaria Gregorio Marañón, 28007 Madrid, Spain
| | - Maria Dolores Folgueira
- Microbiology Department, Hospital Universitario 12 de Octubre, Biomedical Research Institute imas12, 28041 Madrid, Spain
- Department of Medicine, School of Medicine, Universidad Complutense, 28040 Madrid, Spain
| | - Juan Carlos Galán
- CIBER de Epidemiología y Salud Pública (CIBERESP), ISCIII, 28029 Madrid, Spain
- Microbiology Service, Hospital Universitario Ramón y Cajal, Instituto Ramón y Cajal de Investigación Sanitaria (IRYCIS), 28034 Madrid, Spain
| | - Carla López-Causapé
- Microbiology Service, Hospital Universitario Son Espases, 07120 Palma de Mallorca, Spain
| | - Rafael Benito-Ruesca
- Microbiology Service, Hospital Clínico Universitario Lozano Blesa, Departamento de Microbiología, Facultad de Medicina, Instituto de Investigación Sanitaria de Aragón, Universidad de Zaragoza, 50009 Zaragoza, Spain
| | - Julia Alcoba-Florez
- Microbiology Service, Hospital Universitario Ntra. Sra de Candelaria, 38010 Santa Cruz de Tenerife, Spain
| | - Fernando Gonzalez Candelas
- CIBER de Epidemiología y Salud Pública (CIBERESP), ISCIII, 28029 Madrid, Spain
- Joint Research Unit Infection and Public Health FISABIO-University of Valencia, Institute for Integrative Systems Biology (I2SysBio), 46020 Valencia, Spain
| | - María de Toro
- Plataforma de Genómica y Bioinformática, Centro de Investigación Biomédica de La Rioja (CIBIR), 26006 Logroño, Spain
| | - Miguel Fajardo
- Microbiology Service, Hospital Universitario de Badajoz, 06080 Badajoz, Spain
| | - Carmen Ezpeleta
- Complejo Hospitalario de Navarra and Navarra De Servicios Y Tecnologías S A (NASERTIC), 31008 Pamplona, Spain
| | - Fernando Lázaro
- Microbiology Service, Hospital Universitario La Paz, 28046 Madrid, Spain
| | - Sonia Pérez Castro
- Microbiology Service, Complexo Hospitalario Universitario de Vigo, 36204 Vigo, Spain
| | - Isabel Cuesta
- Bioinformatics Unit, Unidades Centrales Científico Técnicas, Instituto de Salud Carlos III, 28222 Majadahonda, Spain
| | - Angel Zaballos
- Genomics Unit, Unidades Centrales Científico Técnicas, Instituto de Salud Carlos III, 28222 Majadahonda, Spain
| | - Francisco Pozo
- Respiratory Viruses and Influenza Unit, National Centre for Microbiology, Instituto de Salud Carlos III, 28222 Majadahonda, Spain
- CIBER de Epidemiología y Salud Pública (CIBERESP), ISCIII, 28029 Madrid, Spain
| | - Inmaculada Casas
- Respiratory Viruses and Influenza Unit, National Centre for Microbiology, Instituto de Salud Carlos III, 28222 Majadahonda, Spain
- CIBER de Epidemiología y Salud Pública (CIBERESP), ISCIII, 28029 Madrid, Spain
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