Genomic epidemiology of SARS-CoV-2 transmission lineages in Ecuador.
Gutierrez B., Márquez S., Prado-Vivar B., Becerra-Wong M., Guadalupe JJ., Candido DDS., Fernandez-Cadena JC., Morey-Leon G., Armas-Gonzalez R., Andrade-Molina DM., Bruno A., De Mora D., Olmedo M., Portugal D., Gonzalez M., Orlando A., Drexler JF., Moreira-Soto A., Sander A-L., Brünink S., Kühne A., Patiño L., Carrazco-Montalvo A., Mestanza O., Zurita J., Sevillano G., Du Plessis L., McCrone JT., Coloma J., Trueba G., Barragán V., Rojas-Silva P., Grunauer M., Kraemer MUG., Faria NR., Escalera-Zamudio M., Pybus OG., Cárdenas P.
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.