Whole Sequencing and Detailed Analysis of SARS-CoV-2 Genomes in Southeast Spain: Identification of Recurrent Mutations in the 20E (EU1) Variant with Some Clinical Implications
During the COVID-19 pandemic caused by SARS-CoV-2, new waves have been associated with new variants and have the potential to escape vaccinations. Therefore, it is useful to conduct retrospective genomic surveillance research. Herein, we present a detailed analysis of 88 SARS-CoV-2 genomes belonging...
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| Format: | Article |
| Language: | English |
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MDPI AG
2023-03-01
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| Series: | Diseases |
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| Online Access: | https://www.mdpi.com/2079-9721/11/2/54 |
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| author | María José López-Andreo María Rosario Vicente-Romero Enrique Bernal Inmaculada Navarro-González Francisco Salazar-Martínez Vanesa Cánovas-Cánovas Cristina Gil-Ortuño María Gema Riquelme-Rocamora Francisco Solano Francisco Javier Ibáñez-López Cristina Tomás Carmen Candel-Pérez Santiago Pérez-Parra César Flores-Flores |
| author_facet | María José López-Andreo María Rosario Vicente-Romero Enrique Bernal Inmaculada Navarro-González Francisco Salazar-Martínez Vanesa Cánovas-Cánovas Cristina Gil-Ortuño María Gema Riquelme-Rocamora Francisco Solano Francisco Javier Ibáñez-López Cristina Tomás Carmen Candel-Pérez Santiago Pérez-Parra César Flores-Flores |
| author_sort | María José López-Andreo |
| collection | DOAJ |
| description | During the COVID-19 pandemic caused by SARS-CoV-2, new waves have been associated with new variants and have the potential to escape vaccinations. Therefore, it is useful to conduct retrospective genomic surveillance research. Herein, we present a detailed analysis of 88 SARS-CoV-2 genomes belonging to samples taken from COVID-19 patients from October 2020 to April 2021 at the “Reina Sofía” Hospital (Murcia, Spain) focused to variant appeared later. The results at the mentioned stage show the turning point since the 20E (EU1) variant was still prevalent (71.6%), but Alpha was bursting to 14.8%. Concern mutations have been found in 5 genomes classified as 20E (EU1), which were not characteristic of this still little evolved variant. Most of those mutations are found in the spike protein, namely Δ69–70, E484K, Q675H and P681H. However, a relevant deletion in ORF1a at positions 3675–3677 was also identified. These mutations have been reported in many later SARS-CoV-2 lineages, including Omicron. Taken together, our data suggest that preferential emergence mutations could already be present in the early converging evolution. Aside from this, the molecular information has been contrasted with clinical data. Statistical analyses suggest that the correlation between age and severity criteria is significantly higher in the viral samples with more accumulated changes. |
| first_indexed | 2024-03-11T02:35:21Z |
| format | Article |
| id | doaj.art-f5632e3655cd48dab08164b28c636c6e |
| institution | Directory Open Access Journal |
| issn | 2079-9721 |
| language | English |
| last_indexed | 2024-03-11T02:35:21Z |
| publishDate | 2023-03-01 |
| publisher | MDPI AG |
| record_format | Article |
| series | Diseases |
| spelling | doaj.art-f5632e3655cd48dab08164b28c636c6e2023-11-18T10:01:45ZengMDPI AGDiseases2079-97212023-03-011125410.3390/diseases11020054Whole Sequencing and Detailed Analysis of SARS-CoV-2 Genomes in Southeast Spain: Identification of Recurrent Mutations in the 20E (EU1) Variant with Some Clinical ImplicationsMaría José López-Andreo0María Rosario Vicente-Romero1Enrique Bernal2Inmaculada Navarro-González3Francisco Salazar-Martínez4Vanesa Cánovas-Cánovas5Cristina Gil-Ortuño6María Gema Riquelme-Rocamora7Francisco Solano8Francisco Javier Ibáñez-López9Cristina Tomás10Carmen Candel-Pérez11Santiago Pérez-Parra12César Flores-Flores13Servicio de Biología Molecular, Área Científica y Técnica de Investigación (ACTI), Universidad de Murcia, 30100 Murcia, SpainLaboratorio de Microbiología del Hospital General Universitario Reina Sofía de Murcia, 30003 Murcia, SpainLaboratorio de Microbiología del Hospital General Universitario Reina Sofía de Murcia, 30003 Murcia, SpainServicio de Biología Molecular, Área Científica y Técnica de Investigación (ACTI), Universidad de Murcia, 30100 Murcia, SpainServicio de Biología Molecular, Área Científica y Técnica de Investigación (ACTI), Universidad de Murcia, 30100 Murcia, SpainServicio de Biología Molecular, Área Científica y Técnica de Investigación (ACTI), Universidad de Murcia, 30100 Murcia, SpainServicio de Biología Molecular, Área Científica y Técnica de Investigación (ACTI), Universidad de Murcia, 30100 Murcia, SpainServicio de Biología Molecular, Área Científica y Técnica de Investigación (ACTI), Universidad de Murcia, 30100 Murcia, SpainDepartamento de Bioquímica y Biología Molecular B e Inmunología, Universidad de Murcia, 30100 Murcia, SpainSección de Apoyo Estadístico, Servicio de Investigación Biosanitaria, Área Científica y Técnica de Investigación (ACTI), Universidad de Murcia, 30100 Murcia, SpainLaboratorio de Microbiología del Hospital General Universitario Reina Sofía de Murcia, 30003 Murcia, SpainLaboratorio de Microbiología del Hospital General Universitario Reina Sofía de Murcia, 30003 Murcia, SpainHospital General Universitario Santa Lucía, 30202 Cartagena, SpainServicio de Biología Molecular, Área Científica y Técnica de Investigación (ACTI), Universidad de Murcia, 30100 Murcia, SpainDuring the COVID-19 pandemic caused by SARS-CoV-2, new waves have been associated with new variants and have the potential to escape vaccinations. Therefore, it is useful to conduct retrospective genomic surveillance research. Herein, we present a detailed analysis of 88 SARS-CoV-2 genomes belonging to samples taken from COVID-19 patients from October 2020 to April 2021 at the “Reina Sofía” Hospital (Murcia, Spain) focused to variant appeared later. The results at the mentioned stage show the turning point since the 20E (EU1) variant was still prevalent (71.6%), but Alpha was bursting to 14.8%. Concern mutations have been found in 5 genomes classified as 20E (EU1), which were not characteristic of this still little evolved variant. Most of those mutations are found in the spike protein, namely Δ69–70, E484K, Q675H and P681H. However, a relevant deletion in ORF1a at positions 3675–3677 was also identified. These mutations have been reported in many later SARS-CoV-2 lineages, including Omicron. Taken together, our data suggest that preferential emergence mutations could already be present in the early converging evolution. Aside from this, the molecular information has been contrasted with clinical data. Statistical analyses suggest that the correlation between age and severity criteria is significantly higher in the viral samples with more accumulated changes.https://www.mdpi.com/2079-9721/11/2/54SARS-CoV-2 variantsCOVID-19concern mutationsgenomic sequencesclinical implications |
| spellingShingle | María José López-Andreo María Rosario Vicente-Romero Enrique Bernal Inmaculada Navarro-González Francisco Salazar-Martínez Vanesa Cánovas-Cánovas Cristina Gil-Ortuño María Gema Riquelme-Rocamora Francisco Solano Francisco Javier Ibáñez-López Cristina Tomás Carmen Candel-Pérez Santiago Pérez-Parra César Flores-Flores Whole Sequencing and Detailed Analysis of SARS-CoV-2 Genomes in Southeast Spain: Identification of Recurrent Mutations in the 20E (EU1) Variant with Some Clinical Implications Diseases SARS-CoV-2 variants COVID-19 concern mutations genomic sequences clinical implications |
| title | Whole Sequencing and Detailed Analysis of SARS-CoV-2 Genomes in Southeast Spain: Identification of Recurrent Mutations in the 20E (EU1) Variant with Some Clinical Implications |
| title_full | Whole Sequencing and Detailed Analysis of SARS-CoV-2 Genomes in Southeast Spain: Identification of Recurrent Mutations in the 20E (EU1) Variant with Some Clinical Implications |
| title_fullStr | Whole Sequencing and Detailed Analysis of SARS-CoV-2 Genomes in Southeast Spain: Identification of Recurrent Mutations in the 20E (EU1) Variant with Some Clinical Implications |
| title_full_unstemmed | Whole Sequencing and Detailed Analysis of SARS-CoV-2 Genomes in Southeast Spain: Identification of Recurrent Mutations in the 20E (EU1) Variant with Some Clinical Implications |
| title_short | Whole Sequencing and Detailed Analysis of SARS-CoV-2 Genomes in Southeast Spain: Identification of Recurrent Mutations in the 20E (EU1) Variant with Some Clinical Implications |
| title_sort | whole sequencing and detailed analysis of sars cov 2 genomes in southeast spain identification of recurrent mutations in the 20e eu1 variant with some clinical implications |
| topic | SARS-CoV-2 variants COVID-19 concern mutations genomic sequences clinical implications |
| url | https://www.mdpi.com/2079-9721/11/2/54 |
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