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

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

Research output: Contribution to journalArticlepeer-review

11 Scopus citations


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.

Original languageEnglish
Article numberA1343
JournalVirus Evolution
Issue number2
StatePublished - 2021


  • Molecular epidemiology
  • Phylogenetics
  • Phylogeography
  • SARS-CoV-2
  • Transmission lineages


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