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Genomic Epidemiology of SARS-CoV-2 in Madrid, Spain, during the First Wave of the Pandemic: Fast Spread and Early Dominance by D614G Variants

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) was first detected in Madrid, Spain, on 25 February 2020. It increased in frequency very fast and by the end of May more than 70,000 cases had been confirmed by reverse transcription-polymerase chain reaction (RT-PCR). To study the lineage...

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Autores principales: Viedma, Esther, Dahdouh, Elias, González-Alba, José María, González-Bodi, Sara, Martínez-García, Laura, Lázaro-Perona, Fernando, Recio, Raúl, Rodríguez-Tejedor, María, Folgueira, María Dolores, Cantón, Rafael, Delgado, Rafael, García-Rodríguez, Julio, Galán, Juan Carlos, Mingorance, Jesús
Formato: Online Artículo Texto
Lenguaje:English
Publicado: MDPI 2021
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7926973/
https://www.ncbi.nlm.nih.gov/pubmed/33671631
http://dx.doi.org/10.3390/microorganisms9020454
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author Viedma, Esther
Dahdouh, Elias
González-Alba, José María
González-Bodi, Sara
Martínez-García, Laura
Lázaro-Perona, Fernando
Recio, Raúl
Rodríguez-Tejedor, María
Folgueira, María Dolores
Cantón, Rafael
Delgado, Rafael
García-Rodríguez, Julio
Galán, Juan Carlos
Mingorance, Jesús
author_facet Viedma, Esther
Dahdouh, Elias
González-Alba, José María
González-Bodi, Sara
Martínez-García, Laura
Lázaro-Perona, Fernando
Recio, Raúl
Rodríguez-Tejedor, María
Folgueira, María Dolores
Cantón, Rafael
Delgado, Rafael
García-Rodríguez, Julio
Galán, Juan Carlos
Mingorance, Jesús
author_sort Viedma, Esther
collection PubMed
description Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) was first detected in Madrid, Spain, on 25 February 2020. It increased in frequency very fast and by the end of May more than 70,000 cases had been confirmed by reverse transcription-polymerase chain reaction (RT-PCR). To study the lineages and the diversity of the viral population during this first epidemic wave in Madrid we sequenced 224 SARS-CoV-2 viral genomes collected from three hospitals from February to May 2020. All the known major lineages were found in this set of samples, though B.1 and B.1.5 were the most frequent ones, accounting for more than 60% of the sequences. In parallel with the B lineages and sublineages, the D614G mutation in the Spike protein sequence was detected soon after the detection of the first coronavirus disease 19 (COVID-19) case in Madrid and in two weeks became dominant, being found in 80% of the samples and remaining at this level during all the study periods. The lineage composition of the viral population found in Madrid was more similar to the European population than to the publicly available Spanish data, underlining the role of Madrid as a national and international transport hub. In agreement with this, phylodynamic analysis suggested multiple independent entries before the national lockdown and air transportation restrictions.
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spelling pubmed-79269732021-03-04 Genomic Epidemiology of SARS-CoV-2 in Madrid, Spain, during the First Wave of the Pandemic: Fast Spread and Early Dominance by D614G Variants Viedma, Esther Dahdouh, Elias González-Alba, José María González-Bodi, Sara Martínez-García, Laura Lázaro-Perona, Fernando Recio, Raúl Rodríguez-Tejedor, María Folgueira, María Dolores Cantón, Rafael Delgado, Rafael García-Rodríguez, Julio Galán, Juan Carlos Mingorance, Jesús Microorganisms Article Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) was first detected in Madrid, Spain, on 25 February 2020. It increased in frequency very fast and by the end of May more than 70,000 cases had been confirmed by reverse transcription-polymerase chain reaction (RT-PCR). To study the lineages and the diversity of the viral population during this first epidemic wave in Madrid we sequenced 224 SARS-CoV-2 viral genomes collected from three hospitals from February to May 2020. All the known major lineages were found in this set of samples, though B.1 and B.1.5 were the most frequent ones, accounting for more than 60% of the sequences. In parallel with the B lineages and sublineages, the D614G mutation in the Spike protein sequence was detected soon after the detection of the first coronavirus disease 19 (COVID-19) case in Madrid and in two weeks became dominant, being found in 80% of the samples and remaining at this level during all the study periods. The lineage composition of the viral population found in Madrid was more similar to the European population than to the publicly available Spanish data, underlining the role of Madrid as a national and international transport hub. In agreement with this, phylodynamic analysis suggested multiple independent entries before the national lockdown and air transportation restrictions. MDPI 2021-02-22 /pmc/articles/PMC7926973/ /pubmed/33671631 http://dx.doi.org/10.3390/microorganisms9020454 Text en © 2021 by the authors. Licensee MDPI, Basel, Switzerland. This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY) license (http://creativecommons.org/licenses/by/4.0/).
spellingShingle Article
Viedma, Esther
Dahdouh, Elias
González-Alba, José María
González-Bodi, Sara
Martínez-García, Laura
Lázaro-Perona, Fernando
Recio, Raúl
Rodríguez-Tejedor, María
Folgueira, María Dolores
Cantón, Rafael
Delgado, Rafael
García-Rodríguez, Julio
Galán, Juan Carlos
Mingorance, Jesús
Genomic Epidemiology of SARS-CoV-2 in Madrid, Spain, during the First Wave of the Pandemic: Fast Spread and Early Dominance by D614G Variants
title Genomic Epidemiology of SARS-CoV-2 in Madrid, Spain, during the First Wave of the Pandemic: Fast Spread and Early Dominance by D614G Variants
title_full Genomic Epidemiology of SARS-CoV-2 in Madrid, Spain, during the First Wave of the Pandemic: Fast Spread and Early Dominance by D614G Variants
title_fullStr Genomic Epidemiology of SARS-CoV-2 in Madrid, Spain, during the First Wave of the Pandemic: Fast Spread and Early Dominance by D614G Variants
title_full_unstemmed Genomic Epidemiology of SARS-CoV-2 in Madrid, Spain, during the First Wave of the Pandemic: Fast Spread and Early Dominance by D614G Variants
title_short Genomic Epidemiology of SARS-CoV-2 in Madrid, Spain, during the First Wave of the Pandemic: Fast Spread and Early Dominance by D614G Variants
title_sort genomic epidemiology of sars-cov-2 in madrid, spain, during the first wave of the pandemic: fast spread and early dominance by d614g variants
topic Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7926973/
https://www.ncbi.nlm.nih.gov/pubmed/33671631
http://dx.doi.org/10.3390/microorganisms9020454
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