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

Gutierrez B.; Márquez S.; Prado-Vivar B.; Becerra-Wong M.; Guadalupe J.J.; da Silva Candido D.; Fernandez-Cadena J.C.; Morey-Leon G.; Armas-Gonzalez R.; Andrade-Molina D.M.; Bruno A.; de Mora D.; Olmedo M.; Portugal D.; Gonzalez M.; Orlando A.; Drexler J.F.; 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 J.T.; Coloma J.; Trueba G.; Barragán V.; Rojas-Silva P.; Grunauer M.; Kraemer M.U.G.; Faria N.R.; Escalera-Zamudio M.; Pybus O.G.; Cárdenas P. · Virus Evolution (2021) · DOI: 10.1093/ve/veab051

Resumen

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. © The Author(s) 2021. Published by Oxford University Press.