The first wave of the Spanish COVID-19 epidemic was associated with early introductions and fast spread of a dominating genetic variant
Authors: López Mariana G. , Chiner-Oms Álvaro , de Viedma Darío García , 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 , Zaldumbide Maitane Aranzamendi , Bea-Escudero María Pilar , Boga Jose Antonio , Bordoy Antoni E. , Canut-Blasco Andrés , Carvajal Ana , Eguiluz Gustavo Cilla , Rodríguez Maria Luz Cordón , Costa-Alcalde José J. , de Toro María , de Toro Peinado Inmaculada , del Pozo Jose Luis , Duchêne Sebastián , Fernández-Pinero Jovita , Escrivá Begoña Fuster , Cardona Concepción Gimeno , Galán Verónica González , Jiménez Nieves Gonzalo , Crespo Silvia Hernáez , Herranz Marta , Lepe José Antonio , López-Hontangas José Luis , Marcos Maria Ángeles , Martín Vicente , Martró Elisa , Beamonte Ana Milagro , Ros Milagrosa Montes , Moreno-Muñoz Rosario , Navarro David , Navarro-Marí José María , Not Anna , Oliver Antonio , Palop-Borrás Begoña , Grande Mónica Parra , Pedrosa-Corral Irene , Gonzalez Maria Carmen Perez , Pérez-Lago Laura , Vázquez Luis Piñeiro , Rabella Nuria , Reina Jordi , Rezusta Antonio , Fonseca Lorena Robles , Rodríguez-Villodres Ángel , Sanbonmatsu-Gámez Sara , Sicilia Jon , Balaguer María Dolores Tirado , Torres Ignacio , Tristancho Alexander , Marimón José María , Coscolla Mireia , González-Candelas Fernando , Comas Iñaki 
Published: December 2020

The COVID-19 pandemic has shaken the world since the beginning of 2020. Spain is among the European countries with the highest incidence of the disease during the first pandemic wave. We established a multidisciplinar consortium to monitor and study the evolution of the epidemic, with the aim of contributing to decision making and stopping rapid spreading across the country. We present the results for 2170 sequences from the first wave of the SARS-Cov-2 epidemic in Spain and representing 12% of diagnosed cases until 14th March. This effort allows us to document at least 500 initial introductions, between early February-March from multiple international sources. Importantly, we document the early raise of two dominant genetic variants in Spain (Spanish Epidemic Clades), named SEC7 and SEC8, likely amplified by superspreading events. In sharp contrast to other non-Asian countries those two variants were closely related to the initial variants of SARS-CoV-2 described in Asia and represented 40% of the genome sequences analyzed. The two dominant SECs were widely spread across the country compared to other genetic variants with SEC8 reaching a 60% prevalence just before the lockdown. Employing Bayesian phylodynamic analysis, we inferred a reduction in the effective reproductive number of these two SECs from around 2.5 to below 0.5 after the implementation of strict public-health interventions in mid March. The effects of lockdown on the genetic variants of the virus are reflected in the general replacement of preexisting SECs by a new variant at the beginning of the summer season. Our results reveal a significant difference in the genetic makeup of the epidemic in Spain and support the effectiveness of lockdown measures in controlling virus spread even for the most successful genetic variants. Finally, earlier control of SEC7 and particularly SEC8 might have reduced the incidence and impact of COVID-19 in our country.