Cost-Effective Method to Perform SARS-CoV-2 Variant Surveillance: Detection of Alpha, Gamma, Lambda, Delta, Epsilon, and Zeta in Argentina

SARS-CoV-2 variants with concerning characteristics have emerged since the end of 2020. Surveillance of SARS-CoV-2 variants was performed on a total of 4,851 samples from the capital city and 10 provinces of Argentina, during 51 epidemiological weeks (EWs) that covered the end of the first wave and...

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Autores principales: Proyecto Argentino Interinstitucional de genómica de SARS-CoV-2, Posner, Victoria María, Villanova, Gabriela Vanina, Acosta, Julián, Cavatorta, Ana Laura
Lenguaje:Inglés
Publicado: Frontiers Media 2022
Materias:
SARS-CoV-2
Variants
South America
Surveillance
Spike sequences
Acceso en línea:http://hdl.handle.net/2133/23407
http://hdl.handle.net/2133/23407
Aporte de:
Repositorio Hipermedial de la Universidad Nacional de Rosario (UNR) de Universidad Nacional de Rosario
id I15-R121-2133-23407
record_format dspace
institution Universidad Nacional de Rosario
institution_str I-15
repository_str R-121
collection Repositorio Hipermedial de la Universidad Nacional de Rosario (UNR)
language Inglés
orig_language_str_mv eng
topic SARS-CoV-2
Variants
South America
Surveillance
Spike sequences
spellingShingle SARS-CoV-2
Variants
South America
Surveillance
Spike sequences
Proyecto Argentino Interinstitucional de genómica de SARS-CoV-2
Posner, Victoria María
Villanova, Gabriela Vanina
Acosta, Julián
Cavatorta, Ana Laura
Cost-Effective Method to Perform SARS-CoV-2 Variant Surveillance: Detection of Alpha, Gamma, Lambda, Delta, Epsilon, and Zeta in Argentina
topic_facet SARS-CoV-2
Variants
South America
Surveillance
Spike sequences
description SARS-CoV-2 variants with concerning characteristics have emerged since the end of 2020. Surveillance of SARS-CoV-2 variants was performed on a total of 4,851 samples from the capital city and 10 provinces of Argentina, during 51 epidemiological weeks (EWs) that covered the end of the first wave and the ongoing second wave of the COVID-19 pandemic in the country (EW 44/2020 to EW 41/2021). The surveillance strategy was mainly based on Sanger sequencing of a Spike coding region that allows the identification of signature mutations associated with variants. In addition, whole-genome sequences were obtained from 637 samples. The main variants found were Gamma and Lambda, and to a lesser extent, Alpha, Zeta, and Epsilon, and more recently, Delta. Whereas, Gamma dominated in different regions of the country, both Gamma and Lambda prevailed in the most populated area, the metropolitan region of Buenos Aires. The lineages that circulated on the first wave were replaced by emergent variants in a term of a few weeks. At the end of the ongoing second wave, Delta began to be detected, replacing Gamma and Lambda. This scenario is consistent with the Latin American variant landscape, so far characterized by a concurrent increase in Delta circulation and a stabilization in the number of cases. The cost-effective surveillance protocol presented here allowed for a rapid response in a resource-limited setting, added information on the expansion of Lambda in South America, and contributed to the implementation of public health measures to control the disease spread in Argentina.
author Proyecto Argentino Interinstitucional de genómica de SARS-CoV-2
Posner, Victoria María
Villanova, Gabriela Vanina
Acosta, Julián
Cavatorta, Ana Laura
author_facet Proyecto Argentino Interinstitucional de genómica de SARS-CoV-2
Posner, Victoria María
Villanova, Gabriela Vanina
Acosta, Julián
Cavatorta, Ana Laura
author_sort Proyecto Argentino Interinstitucional de genómica de SARS-CoV-2
title Cost-Effective Method to Perform SARS-CoV-2 Variant Surveillance: Detection of Alpha, Gamma, Lambda, Delta, Epsilon, and Zeta in Argentina
title_short Cost-Effective Method to Perform SARS-CoV-2 Variant Surveillance: Detection of Alpha, Gamma, Lambda, Delta, Epsilon, and Zeta in Argentina
title_full Cost-Effective Method to Perform SARS-CoV-2 Variant Surveillance: Detection of Alpha, Gamma, Lambda, Delta, Epsilon, and Zeta in Argentina
title_fullStr Cost-Effective Method to Perform SARS-CoV-2 Variant Surveillance: Detection of Alpha, Gamma, Lambda, Delta, Epsilon, and Zeta in Argentina
title_full_unstemmed Cost-Effective Method to Perform SARS-CoV-2 Variant Surveillance: Detection of Alpha, Gamma, Lambda, Delta, Epsilon, and Zeta in Argentina
title_sort cost-effective method to perform sars-cov-2 variant surveillance: detection of alpha, gamma, lambda, delta, epsilon, and zeta in argentina
publisher Frontiers Media
publishDate 2022
url http://hdl.handle.net/2133/23407
http://hdl.handle.net/2133/23407
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