enomic epidemiology of SARS-CoV-2 transmission lineages in Ecuado

Author(s):Show less -

Gutierrez, Bernardo ^{[1, 2]} ; Marquez, Sully ^[3] ; Prado-Vivar, Belen ^[3] ; Becerra-Wong, Monica ^[3] ; Jose Guadalupe, Juan ^[4] ; da Silva Candido, Darlan ^[1] ; Carlos Fernandez-Cadena, Juan ^[5] ; Morey-Leon, Gabriel ^[6] ; Armas-Gonzalez, Ruben ^[7] ; Madeleiny Andrade-Molina, Derly ^[5] ; Bruno, Alfredo ^{[8, 9]} ; de Mora, Domenica ^[8] ; Olmedo, Maritza ^[8] ; Portugal, Denisse ^[8] ; Gonzalez, Manuel ^[8] ; Orlando, Alberto ^[8] ; Felix Drexler, Jan ^{[10, 11, 12, 13]} ; Moreira-Soto, Andres ^{[10, 11, 12, 13]} ; Sander, Anna-Lena ^{[10, 11, 12, 13]} ; Brunink, Sebastian ^{[10, 11, 12, 13]} ; Kuhne, Arne ^{[10, 11, 12, 13]} ; Patino, Leandro ^[8] ; Carrazco-Montalvo, Andres ^[14] ; Mestanza, Orson ^[15] ; Zurita, Jeannete ^{[16, 17]} ; Sevillano, Gabriela ^[17] ; du Plessis, Louis ^[1] ; McCrone, John T. ^[18] ; Coloma, Josefina ^[19] ; Trueba, Gabriel ^[3] ; Barragan, Veronica ^[3] ; Rojas-Silva, Patricio ^[3] ; Grunauer, Michelle ^[20] ; Kraemer, Moritz U. G. ^[1] ; Faria, Nuno R. ^{[21, 1]} ; Escalera-Zamudio, Marina ^[1] ; Pybus, Oliver G. ^{[1, 22]} ; Cardenas, Paul ^[3]

Affiliation:Show less -

^[1] Univ Oxford, Dept Zool, Oxford OX1 3SY, Oxon - England

^[2] Univ San Francisco Quito, Colegio Ciencias Biol & Ambientales, Quito 170901 - Ecuador

^[3] Univ San Francisco Quito, Inst Microbiol, Quito 170901 - Ecuador

^[4] Univ San Francisco Quito, Lab Biotecnol Vegetal, Quito 170901 - Ecuador

^[5] Univ Especialidades Espiritu Santo, Fac Med Sci, Omics Sci Lab, Samborondon 092301 - Ecuador

^[6] Univ Guayaquil, Fac Med Sci, Guayaquil 090613 - Ecuador

^[7] Escuela Super Politecn Litoral, Fac Sci, Guayaquil 090112 - Ecuador

^[8] Inst Nacl Invest Salud Publ, Guayaquil 3961 - Ecuador

^[9] Univ Agr Ecuador, Guayaquil 090104 - Ecuador

^[10] Charite Univ Med Berlin, Inst Virol, D-10117 Berlin - Germany

^[11] Free Univ Berlin, D-10117 Berlin - Germany

^[12] Humboldt Univ, D-10117 Berlin - Germany

^[13] Berlin Inst Hlth, D-10117 Berlin - Germany

^[14] Inst Nacl Invest Salud Publ, Quito 170403 - Ecuador

^[15] Inst Nacl Salud Nino San Borja, Serv Genet, Lima 15037 - Peru

^[16] Pontificia Univ Catolica Ecuador, Fac Med, Quito 170143 - Ecuador

^[17] Zurita & Zurita Labs, Unidad Invest Biomed, Quito 170104 - Ecuador

^[18] Univ Edinburgh, Inst Evolutionary Biol, Edinburgh EH9 3JW, Midlothian - Scotland

^[19] Univ Calif Berkeley, Sch Publ Hlth, Berkeley, CA 94704 - USA

^[20] Univ San Francisco Quito, Escuela Med, Quito 170901 - Ecuador

^[21] Imperial Coll London, MRC Ctr Global Infect Dis Anal, J IDEA, London SW7 2AZ - England

^[22] Royal Vet Coll London, Dept Pathobiol & Populat Sci, London NW1 0TU - England

• Document type: Journal article
• Source: VIRUS EVOLUTION; v. 7, n. 2 DEC 2021.
• Web of Science Citations: 0

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. (AU)

• FAPESP's process: 18/14389-0 - Brazil-UK Centre for Arbovirus Discovery, Diagnosis, Genomics and Epidemiology (CADDE)
• Grantee: Ester Cerdeira Sabino
• Support Opportunities: Research Projects - Thematic Grants