Genomic epidemiology of SARS-CoV-2 transmission lineages in Ecuador

Gutierrez, Bernardo; Márquez, Sully; Prado-Vivar, Belén; Becerra-Wong, Mónica; Guadalupe, Juan José; da Silva Candido, Darlan; Fernandez-Cadena, Juan Carlos; Morey-Leon, Gabriel; Armas-Gonzalez, Rubén; Andrade-Molina, Derly Madeleiny; Bruno, Alfredo; de Mora, Domenica; Olmedo, Maritza; Portugal, Denisse; Gonzalez, Manuel; Orlando, Alberto; Drexler, Jan Felix; Moreira-Soto, Andres; Sander, Anna-Lena; Brünink, Sebastian; Kühne, Arne; Patiño, Leandro; Carrazco-Montalvo, Andrés; Mestanza, Orson; Zurita, Jeannete; Sevillano, Gabriela; du Plessis, Louis; McCrone, John T.; Coloma, Josefina; Trueba, Gabriel; Barragán, Verónica; Rojas-Silva, Patricio; Grunauer, Michelle; Kraemer, Moritz U.G.; Faria, Nuno R.; Escalera-Zamudio, Marina; Pybus, Oliver G.; Cárdenas, Paúl

Characterisation of 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 COVID-19 pandemic. We generate and analyse 160 whole genome sequences sampled from all provinces of Ecuador in 2020. Molecular clock and phylgeographic 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 (NPIs), with differential degrees of persistence and national dissemination.