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SARS-CoV-2 genome sequencing from COVID-19 in Ecuadorian patients: a whole country analysis

SARS-CoV-2, the etiological agent of COVID-19, was first described in Wuhan, China in December 2019 and has now spread globally. Ecuador was the second country in South America to confirm cases and Guayaquil was one of the first cities in the world to experience high mortality due to COVID-19. The a...

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Autores principales: Márquez, Sully, Prado-Vivar, Belén, Guadalupe, Juan José, Becerra-Wong, Mónica, Gutierrez, Bernardo, Fernández-Cadena, Juan Carlos, Andrade-Molina, Derly, Morey-Leon, Gabriel, Moncayo, Miguel, Guevara, Rommel, Coloma, Josefina, Trueba, Gabriel, Grunauer, Michelle, Barragán, Verónica, Rojas-Silva, Patricio, Cárdenas, Paúl
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Cold Spring Harbor Laboratory 2021
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8010754/
https://www.ncbi.nlm.nih.gov/pubmed/33791722
http://dx.doi.org/10.1101/2021.03.19.21253620
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author Márquez, Sully
Prado-Vivar, Belén
Guadalupe, Juan José
Becerra-Wong, Mónica
Gutierrez, Bernardo
Fernández-Cadena, Juan Carlos
Andrade-Molina, Derly
Morey-Leon, Gabriel
Moncayo, Miguel
Guevara, Rommel
Coloma, Josefina
Trueba, Gabriel
Grunauer, Michelle
Barragán, Verónica
Rojas-Silva, Patricio
Cárdenas, Paúl
author_facet Márquez, Sully
Prado-Vivar, Belén
Guadalupe, Juan José
Becerra-Wong, Mónica
Gutierrez, Bernardo
Fernández-Cadena, Juan Carlos
Andrade-Molina, Derly
Morey-Leon, Gabriel
Moncayo, Miguel
Guevara, Rommel
Coloma, Josefina
Trueba, Gabriel
Grunauer, Michelle
Barragán, Verónica
Rojas-Silva, Patricio
Cárdenas, Paúl
author_sort Márquez, Sully
collection PubMed
description SARS-CoV-2, the etiological agent of COVID-19, was first described in Wuhan, China in December 2019 and has now spread globally. Ecuador was the second country in South America to confirm cases and Guayaquil was one of the first cities in the world to experience high mortality due to COVID-19. The aim of this study was to describe the lineages circulating throughout the country and to compare the mutations in local variants, to the reference strain. In this work we used the MinION platform (Oxford Nanopore Technologies) to sequence the whole SARS-CoV-2 genomes of 119 patients from all provinces of Ecuador, using the ARTIC network protocols. Our data from lineage assignment of the one hundred and nineteen whole genomes revealed twenty different lineages. All genomes presented differences in the S gene compared to the Wuhan reference strain, being the D614G amino acid replacement the most common change. The B.1.1.119 lineage was the most frequent and was found in several locations in the Coast and Andean region. Three sequences were assigned to the new B.1.1.7 lineage. Our work is an important contribution to the understanding of the epidemiology of SARS-CoV-2 in Ecuador and South America.
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spelling pubmed-80107542021-04-01 SARS-CoV-2 genome sequencing from COVID-19 in Ecuadorian patients: a whole country analysis Márquez, Sully Prado-Vivar, Belén Guadalupe, Juan José Becerra-Wong, Mónica Gutierrez, Bernardo Fernández-Cadena, Juan Carlos Andrade-Molina, Derly Morey-Leon, Gabriel Moncayo, Miguel Guevara, Rommel Coloma, Josefina Trueba, Gabriel Grunauer, Michelle Barragán, Verónica Rojas-Silva, Patricio Cárdenas, Paúl medRxiv Article SARS-CoV-2, the etiological agent of COVID-19, was first described in Wuhan, China in December 2019 and has now spread globally. Ecuador was the second country in South America to confirm cases and Guayaquil was one of the first cities in the world to experience high mortality due to COVID-19. The aim of this study was to describe the lineages circulating throughout the country and to compare the mutations in local variants, to the reference strain. In this work we used the MinION platform (Oxford Nanopore Technologies) to sequence the whole SARS-CoV-2 genomes of 119 patients from all provinces of Ecuador, using the ARTIC network protocols. Our data from lineage assignment of the one hundred and nineteen whole genomes revealed twenty different lineages. All genomes presented differences in the S gene compared to the Wuhan reference strain, being the D614G amino acid replacement the most common change. The B.1.1.119 lineage was the most frequent and was found in several locations in the Coast and Andean region. Three sequences were assigned to the new B.1.1.7 lineage. Our work is an important contribution to the understanding of the epidemiology of SARS-CoV-2 in Ecuador and South America. Cold Spring Harbor Laboratory 2021-03-24 /pmc/articles/PMC8010754/ /pubmed/33791722 http://dx.doi.org/10.1101/2021.03.19.21253620 Text en https://creativecommons.org/licenses/by-nc-nd/4.0/This work is licensed under a Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International License (https://creativecommons.org/licenses/by-nc-nd/4.0/) , which allows reusers to copy and distribute the material in any medium or format in unadapted form only, for noncommercial purposes only, and only so long as attribution is given to the creator.
spellingShingle Article
Márquez, Sully
Prado-Vivar, Belén
Guadalupe, Juan José
Becerra-Wong, Mónica
Gutierrez, Bernardo
Fernández-Cadena, Juan Carlos
Andrade-Molina, Derly
Morey-Leon, Gabriel
Moncayo, Miguel
Guevara, Rommel
Coloma, Josefina
Trueba, Gabriel
Grunauer, Michelle
Barragán, Verónica
Rojas-Silva, Patricio
Cárdenas, Paúl
SARS-CoV-2 genome sequencing from COVID-19 in Ecuadorian patients: a whole country analysis
title SARS-CoV-2 genome sequencing from COVID-19 in Ecuadorian patients: a whole country analysis
title_full SARS-CoV-2 genome sequencing from COVID-19 in Ecuadorian patients: a whole country analysis
title_fullStr SARS-CoV-2 genome sequencing from COVID-19 in Ecuadorian patients: a whole country analysis
title_full_unstemmed SARS-CoV-2 genome sequencing from COVID-19 in Ecuadorian patients: a whole country analysis
title_short SARS-CoV-2 genome sequencing from COVID-19 in Ecuadorian patients: a whole country analysis
title_sort sars-cov-2 genome sequencing from covid-19 in ecuadorian patients: a whole country analysis
topic Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8010754/
https://www.ncbi.nlm.nih.gov/pubmed/33791722
http://dx.doi.org/10.1101/2021.03.19.21253620
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