The first wave of the COVID-19 epidemic in Spain was associated with early introductions and fast spread of a dominating genetic variant

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

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 (R(e) < 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.