Omicron Sub-Lineages (BA.1.1.529 + BA.*) Current Status in Ecuador

USFQ-COVID-19 Consortium; CRN Influenza y OVR—INSPI

doi:10.3390/v14061177

Omicron Sub-Lineages (BA.1.1.529 + BA.*) Current Status in Ecuador

USFQ-COVID-19 Consortium
, CRN Influenza y OVR—INSPI

Centro de Referencia Nacional de Genómica
Instituto Nacional de Investigación en Salud Pública
Universidad Internacional SEK Ecuador
Universidad Espíritu Santo, Ecuador
Laboratorio INTERLAB
Universidad de Guayaquil
Instituto Nacional de Investigación en Salud Pública “Leopoldo Izquieta Pérez,”

Research output: Contribution to journal › Article › peer-review

11 Scopus citations

Abstract

The Omicron variant of SARS-CoV-2 is the latest pandemic lineage causing COVID-19. Despite having a vaccination rate ≥ 85%, Ecuador recorded a high incidence of Omicron from De-cember 2021 to March 2022. Since Omicron emerged, it has evolved into multiple sub-lineages with distinct prevalence in different regions. In this work, we use all Omicron sequences from Ecuador available at GISAID until March 2022 and the software Nextclade and Pangolin to identify which lineages circulate in this country. We detected 12 different sub-lineages (BA.1, BA.1.1, BA.1.1.1, BA.1.1.14, BA.1.1.2, BA.1.14, BA.1.15, BA.1.16, BA.1.17, BA.1.6, BA.2, BA.2.3), which have been re-ported in Africa, America, Europe, and Asia, suggesting multiple introduction events. Sub-lineages BA.1 and BA.1.1 were the most prevalent. Genomic surveillance must continue to evaluate the dynamics of current sub-lineages, the early introduction of new ones and vaccine efficacy against evolving SARS-CoV-2.

Original language	English
Article number	1177
Journal	Viruses
Volume	14
Issue number	6
DOIs	https://doi.org/10.3390/v14061177
State	Published - Jun 2022

UN SDGs

This output contributes to the following UN Sustainable Development Goals (SDGs)

SDG 3 Good Health and Well-being

Keywords

COVID-19
Ecuador
Omicron
sub-lineages

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10.3390/v14061177

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@article{a4089224926943ddae46dad86859e1f0,

title = "Omicron Sub-Lineages (BA.1.1.529 + BA.*) Current Status in Ecuador",

abstract = "The Omicron variant of SARS-CoV-2 is the latest pandemic lineage causing COVID-19. Despite having a vaccination rate ≥ 85\%, Ecuador recorded a high incidence of Omicron from De-cember 2021 to March 2022. Since Omicron emerged, it has evolved into multiple sub-lineages with distinct prevalence in different regions. In this work, we use all Omicron sequences from Ecuador available at GISAID until March 2022 and the software Nextclade and Pangolin to identify which lineages circulate in this country. We detected 12 different sub-lineages (BA.1, BA.1.1, BA.1.1.1, BA.1.1.14, BA.1.1.2, BA.1.14, BA.1.15, BA.1.16, BA.1.17, BA.1.6, BA.2, BA.2.3), which have been re-ported in Africa, America, Europe, and Asia, suggesting multiple introduction events. Sub-lineages BA.1 and BA.1.1 were the most prevalent. Genomic surveillance must continue to evaluate the dynamics of current sub-lineages, the early introduction of new ones and vaccine efficacy against evolving SARS-CoV-2.",

keywords = "COVID-19, Ecuador, Omicron, sub-lineages",

author = "\{USFQ-COVID-19 Consortium\} and \{CRN Influenza y OVR—INSPI\} and Andr{\'e}s Carrazco-Montalvo and Andr{\'e}s Herrera-Yela and Damaris Alarc{\'o}n-Vallejo and Diana Guti{\'e}rrez-Pallo and Isaac Armend{\'a}riz-Castillo and Derly Andrade-Molina and Karen Mu{\~n}oz-Mawyin and Fern{\'a}ndez-Cadena, \{Juan Carlos\} and Gabriel Morey-Le{\'o}n and Mateo Carvajal and Erika Mu{\~n}oz and Rommel Guevara and Sully M{\'a}rquez and Bel{\'e}n Prado-Vivar and Michelle Grunauer and Gabriel Trueba and Patricio Rojas-Silva and Ver{\'o}nica Barragan and Pa{\'u}l C{\'a}rdenas and Alfredo Bruno and Jimmy Garc{\'e}s and Maritza Olmedo and Michelle P{\'a}ez and Rub{\'e}n Armas-Gonzalez and Leandro Pati{\~n}o",

note = "Publisher Copyright: {\textcopyright} 2022 by the author. Licensee MDPI, Basel, Switzerland.",

year = "2022",

month = jun,

doi = "10.3390/v14061177",

language = "Ingl{\'e}s",

volume = "14",

journal = "Viruses",

issn = "1999-4915",

publisher = "Multidisciplinary Digital Publishing Institute (MDPI)",

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T1 - Omicron Sub-Lineages (BA.1.1.529 + BA.*) Current Status in Ecuador

AU - USFQ-COVID-19 Consortium

AU - CRN Influenza y OVR—INSPI

AU - Carrazco-Montalvo, Andrés

AU - Herrera-Yela, Andrés

AU - Alarcón-Vallejo, Damaris

AU - Gutiérrez-Pallo, Diana

AU - Armendáriz-Castillo, Isaac

AU - Andrade-Molina, Derly

AU - Muñoz-Mawyin, Karen

AU - Fernández-Cadena, Juan Carlos

AU - Morey-León, Gabriel

AU - Carvajal, Mateo

AU - Muñoz, Erika

AU - Guevara, Rommel

AU - Márquez, Sully

AU - Prado-Vivar, Belén

AU - Grunauer, Michelle

AU - Trueba, Gabriel

AU - Rojas-Silva, Patricio

AU - Barragan, Verónica

AU - Cárdenas, Paúl

AU - Bruno, Alfredo

AU - Garcés, Jimmy

AU - Olmedo, Maritza

AU - Páez, Michelle

AU - Armas-Gonzalez, Rubén

AU - Patiño, Leandro

PY - 2022/6

Y1 - 2022/6

N2 - The Omicron variant of SARS-CoV-2 is the latest pandemic lineage causing COVID-19. Despite having a vaccination rate ≥ 85%, Ecuador recorded a high incidence of Omicron from De-cember 2021 to March 2022. Since Omicron emerged, it has evolved into multiple sub-lineages with distinct prevalence in different regions. In this work, we use all Omicron sequences from Ecuador available at GISAID until March 2022 and the software Nextclade and Pangolin to identify which lineages circulate in this country. We detected 12 different sub-lineages (BA.1, BA.1.1, BA.1.1.1, BA.1.1.14, BA.1.1.2, BA.1.14, BA.1.15, BA.1.16, BA.1.17, BA.1.6, BA.2, BA.2.3), which have been re-ported in Africa, America, Europe, and Asia, suggesting multiple introduction events. Sub-lineages BA.1 and BA.1.1 were the most prevalent. Genomic surveillance must continue to evaluate the dynamics of current sub-lineages, the early introduction of new ones and vaccine efficacy against evolving SARS-CoV-2.

AB - The Omicron variant of SARS-CoV-2 is the latest pandemic lineage causing COVID-19. Despite having a vaccination rate ≥ 85%, Ecuador recorded a high incidence of Omicron from De-cember 2021 to March 2022. Since Omicron emerged, it has evolved into multiple sub-lineages with distinct prevalence in different regions. In this work, we use all Omicron sequences from Ecuador available at GISAID until March 2022 and the software Nextclade and Pangolin to identify which lineages circulate in this country. We detected 12 different sub-lineages (BA.1, BA.1.1, BA.1.1.1, BA.1.1.14, BA.1.1.2, BA.1.14, BA.1.15, BA.1.16, BA.1.17, BA.1.6, BA.2, BA.2.3), which have been re-ported in Africa, America, Europe, and Asia, suggesting multiple introduction events. Sub-lineages BA.1 and BA.1.1 were the most prevalent. Genomic surveillance must continue to evaluate the dynamics of current sub-lineages, the early introduction of new ones and vaccine efficacy against evolving SARS-CoV-2.

KW - COVID-19

KW - Ecuador

KW - Omicron

KW - sub-lineages

UR - https://www.scopus.com/pages/publications/85132853923

U2 - 10.3390/v14061177

DO - 10.3390/v14061177

M3 - Artículo

C2 - 35746651

AN - SCOPUS:85132853923

SN - 1999-4915

VL - 14

JO - Viruses

JF - Viruses

IS - 6

M1 - 1177

ER -

Omicron Sub-Lineages (BA.1.1.529 + BA.*) Current Status in Ecuador

Abstract

UN SDGs

Keywords

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