- Gutierrez, Bernardo;
- Márquez, Sully;
- Prado-Vivar, Belén;
- Becerra-Wong, Mónica;
- Guadalupe, Juan;
- Candido, Darlan;
- Fernandez-Cadena, Juan;
- Morey-Leon, Gabriel;
- Armas-Gonzalez, Rubén;
- Andrade-Molina, Derly;
- Bruno, Alfredo;
- De Mora, Domenica;
- Olmedo, Maritza;
- Portugal, Denisse;
- Gonzalez, Manuel;
- Orlando, Alberto;
- Drexler, Jan;
- 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;
- Coloma, Josefina;
- Trueba, Gabriel;
- Barragán, Verónica;
- Rojas-Silva, Patricio;
- Grunauer, Michelle;
- Kraemer, Moritz;
- Faria, Nuno;
- Escalera-Zamudio, Marina;
- Pybus, Oliver;
- Cárdenas, Paúl
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.