Genomic epidemiology of SARS-CoV-2 transmission lineages in Ecuador
Bernardo Gutiérrez, Sully Márquez, Belén Prado-Vivar, Mónica Becerra-Wong, Juan José Guadalupe, Darlan da Silva Cândido, Juan Carlos Fernández‐Cadena, Gabriel Morey-León, Rubén Armas-González, Derly Andrade-Molina, Alfredo Bruno, Doménica de Mora, Maritza Olmedo, Denisse Portugal, Manuel González, Solón Alberto Orlando, Jan Felix Drexler, Andrés Moreira‐Soto, Anna‐Lena Sander, Sebastian Brünink, Arne Kühne, Leandro Patiño, Andrés Carrazco-Montalvo, Orson Mestanza, Jeannete Zurita, Gabriela Sevillano, Louis du Plessis, John T. McCrone, Joséfina Coloma, Gabriel Trueba, Verónica Barragán, Patricio Rojas‐Silva, Michelle Grunauer, Moritz U. G. Kraemer, Nuno R. Faria, Marina Escalera‐Zamudio, Oliver G. Pybus, Paúl Cárdenas
Abstract
Characterisation of severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) genetic diversity through space and time can reveal trends in virus importation and domestic circulation and permit the exploration of questions regarding the early transmission dynamics. Here, we present a detailed description of SARS-CoV-2 genomic epidemiology in Ecuador, one of the hardest hit countries during the early stages of the coronavirus-19 pandemic. We generated and analysed 160 whole genome sequences sampled from all provinces of Ecuador in 2020. Molecular clock and phylogeographic analysis of these sequences in the context of global SARS-CoV-2 diversity enable us to identify and characterise individual transmission lineages within Ecuador, explore their spatiotemporal distributions, and consider their introduction and domestic circulation. Our results reveal a pattern of multiple international importations across the country, with apparent differences between key provinces. Transmission lineages were mostly introduced before the implementation of non-pharmaceutical interventions, with differential degrees of persistence and national dissemination.