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The first wave of the COVID-19 epidemic in Spain was associated with early introductions and fast spread of a dominating genetic variant
Nature Genetics  (IF38.33),  Pub Date : 2021-09-30, DOI: 10.1038/s41588-021-00936-6
Mariana G. López, Álvaro Chiner-Oms, Darío García de Viedma, Paula Ruiz-Rodriguez, Maria Alma Bracho, Irving Cancino-Muñoz, Giuseppe D’Auria, Griselda de Marco, Neris García-González, Galo Adrian Goig, Inmaculada Gómez-Navarro, Santiago Jiménez-Serrano, Llúcia Martinez-Priego, Paula Ruiz-Hueso, Lidia Ruiz-Roldán, Manuela Torres-Puente, Juan Alberola, Eliseo Albert, Maitane Aranzamendi Zaldumbide, María Pilar Bea-Escudero, Jose Antonio Boga, Antoni E. Bordoy, Andrés Canut-Blasco, Ana Carvajal, Gustavo Cilla Eguiluz, Maria Luz Cordón Rodríguez, José J. Costa-Alcalde, María de Toro, Inmaculada de Toro Peinado, Jose Luis del Pozo, Sebastián Duchêne, Jovita Fernández-Pinero, Begoña Fuster Escrivá, Concepción Gimeno Cardona, Verónica González Galán, Nieves Gonzalo Jiménez, Silvia Hernáez Crespo, Marta Herranz, José Antonio Lepe, Carla López-Causapé, José Luis López-Hontangas, Vicente Martín, Elisa Martró, Ana Milagro Beamonte, Milagrosa Montes Ros, Rosario Moreno-Muñoz, David Navarro, José María Navarro-Marí, Anna Not, Antonio Oliver, Begoña Palop-Borrás, Mónica Parra Grande, Irene Pedrosa-Corral, Maria Carmen Pérez González, Laura Pérez-Lago, Mercedes Pérez-Ruiz, Luis Piñeiro Vázquez, Nuria Rabella, Antonio Rezusta, Lorena Robles Fonseca, Ángel Rodríguez-Villodres, Sara Sanbonmatsu-Gámez, Jon Sicilia, Alex Soriano, María Dolores Tirado Balaguer, Ignacio Torres, Alexander Tristancho, José María Marimón, Mireia Coscolla, Fernando González-Candelas, Iñaki Comas

The coronavirus disease 2019 (COVID-19) pandemic has affected the world radically since 2020. Spain was one of the European countries with the highest incidence during the first wave. As a part of a consortium to monitor and study the evolution of the epidemic, we sequenced 2,170 samples, diagnosed mostly before lockdown measures. Here, we identified at least 500 introductions from multiple international sources and documented the early rise of two dominant Spanish epidemic clades (SECs), probably amplified by superspreading events. Both SECs were related closely to the initial Asian variants of SARS-CoV-2 and spread widely across Spain. We inferred a substantial reduction in the effective reproductive number of both SECs due to public-health interventions (Re < 1), also reflected in the replacement of SECs by a new variant over the summer of 2020. In summary, we reveal a notable difference in the initial genetic makeup of SARS-CoV-2 in Spain compared with other European countries and show evidence to support the effectiveness of lockdown measures in controlling virus spread, even for the most successful genetic variants.