Genomic epidemiology of SARS-CoV-2 transmission lineages in Ecuador. Issue 2 (4th June 2021)

• Record Type: Journal Article
• Authors: Gutierrez, Bernardo; Márquez, Sully; Prado-Vivar, Belén; Becerra-Wong, Mónica; Guadalupe, Juan José; Candido, Darlan Da Silva; 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;
• Is Part Of: Virus evolution. Volume 7:Issue 2(2021)
• Publication Date: 2021-06-04
• Subjects: SARS-CoV-2 -- phylogenetics -- molecular epidemiology -- phylogeography -- transmission lineages; Viruses -- Evolution -- Periodicals; 579.2138
• DOI: 10.1093/ve/veab051
• Languages: English
• ISSNs: 2057-1577

Abstract

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.