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Tracking SARS-CoV-2 Variants Using a Rapid Typification Strategy: A Key Tool for Early Detection and Spread Investigation of Omicron in Argentina

SARS-CoV-2 variants of concern (VOC) and interest (VOI) present mutations in reference to the original virus, being more transmissible. We implemented a rapid strategy for the screening of SARS-CoV-2 VOC/VOIs using real time RT-PCR and performed monitoring and surveillance of the variants in our reg...

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Autores principales: Castro, Gonzalo M., Sicilia, Paola, Bolzon, María Laura, Lopez, Laura, Barbás, María Gabriela, Pisano, María Belén, Ré, Viviana E.
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Frontiers Media S.A. 2022
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9157384/
https://www.ncbi.nlm.nih.gov/pubmed/35665324
http://dx.doi.org/10.3389/fmed.2022.851861
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author Castro, Gonzalo M.
Sicilia, Paola
Bolzon, María Laura
Lopez, Laura
Barbás, María Gabriela
Pisano, María Belén
Ré, Viviana E.
author_facet Castro, Gonzalo M.
Sicilia, Paola
Bolzon, María Laura
Lopez, Laura
Barbás, María Gabriela
Pisano, María Belén
Ré, Viviana E.
author_sort Castro, Gonzalo M.
collection PubMed
description SARS-CoV-2 variants of concern (VOC) and interest (VOI) present mutations in reference to the original virus, being more transmissible. We implemented a rapid strategy for the screening of SARS-CoV-2 VOC/VOIs using real time RT-PCR and performed monitoring and surveillance of the variants in our region. Consecutive real-time RT-PCRs for detection of the relevant mutations/deletions present in the Spike protein in VOC/VOIs (TaqMan™ SARS-CoV-2 Mutation Panel, Applied Biosystems) were implemented. A total of 6,640 SARS-CoV-2 RNA samples (Cts < 30) from infected individuals in Central Argentina during 2021 were analyzed using different algorithms that were gradually adapted to the changing scenarios of local variant circulation. The strategy developed allowed the early detection and the identification of VOC/VOIs that circulated through the year, with a 100% of concordance with the WGS. The analyses of the samples showed introductions of VOCs Alpha and Gamma in February and March 2021, respectively. Gamma showed an exponential increase, with a peak of detection in July (72%), being responsible of the second wave of COVID19 in Argentina. Since VOC Delta entered into the region, it increased gradually, together with VOI Lambda, replacing VOC Gamma, until being the main variant (84.9%) on November. By December, these variants were replaced by the emergent VOC Omicron in a term of 2 weeks, producing the third wave. We report a useful tool for VOC/VOI detection, capable to quickly and cost-effectively monitor currently recognized variants in resource-limited settings, which allowed to track the recent expansion of Omicron in our region, and contributed to the implementation of public health measures to control the disease spread.
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spelling pubmed-91573842022-06-02 Tracking SARS-CoV-2 Variants Using a Rapid Typification Strategy: A Key Tool for Early Detection and Spread Investigation of Omicron in Argentina Castro, Gonzalo M. Sicilia, Paola Bolzon, María Laura Lopez, Laura Barbás, María Gabriela Pisano, María Belén Ré, Viviana E. Front Med (Lausanne) Medicine SARS-CoV-2 variants of concern (VOC) and interest (VOI) present mutations in reference to the original virus, being more transmissible. We implemented a rapid strategy for the screening of SARS-CoV-2 VOC/VOIs using real time RT-PCR and performed monitoring and surveillance of the variants in our region. Consecutive real-time RT-PCRs for detection of the relevant mutations/deletions present in the Spike protein in VOC/VOIs (TaqMan™ SARS-CoV-2 Mutation Panel, Applied Biosystems) were implemented. A total of 6,640 SARS-CoV-2 RNA samples (Cts < 30) from infected individuals in Central Argentina during 2021 were analyzed using different algorithms that were gradually adapted to the changing scenarios of local variant circulation. The strategy developed allowed the early detection and the identification of VOC/VOIs that circulated through the year, with a 100% of concordance with the WGS. The analyses of the samples showed introductions of VOCs Alpha and Gamma in February and March 2021, respectively. Gamma showed an exponential increase, with a peak of detection in July (72%), being responsible of the second wave of COVID19 in Argentina. Since VOC Delta entered into the region, it increased gradually, together with VOI Lambda, replacing VOC Gamma, until being the main variant (84.9%) on November. By December, these variants were replaced by the emergent VOC Omicron in a term of 2 weeks, producing the third wave. We report a useful tool for VOC/VOI detection, capable to quickly and cost-effectively monitor currently recognized variants in resource-limited settings, which allowed to track the recent expansion of Omicron in our region, and contributed to the implementation of public health measures to control the disease spread. Frontiers Media S.A. 2022-05-17 /pmc/articles/PMC9157384/ /pubmed/35665324 http://dx.doi.org/10.3389/fmed.2022.851861 Text en Copyright © 2022 Castro, Sicilia, Bolzon, Lopez, Barbás, Pisano and Ré. https://creativecommons.org/licenses/by/4.0/This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) and the copyright owner(s) are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.
spellingShingle Medicine
Castro, Gonzalo M.
Sicilia, Paola
Bolzon, María Laura
Lopez, Laura
Barbás, María Gabriela
Pisano, María Belén
Ré, Viviana E.
Tracking SARS-CoV-2 Variants Using a Rapid Typification Strategy: A Key Tool for Early Detection and Spread Investigation of Omicron in Argentina
title Tracking SARS-CoV-2 Variants Using a Rapid Typification Strategy: A Key Tool for Early Detection and Spread Investigation of Omicron in Argentina
title_full Tracking SARS-CoV-2 Variants Using a Rapid Typification Strategy: A Key Tool for Early Detection and Spread Investigation of Omicron in Argentina
title_fullStr Tracking SARS-CoV-2 Variants Using a Rapid Typification Strategy: A Key Tool for Early Detection and Spread Investigation of Omicron in Argentina
title_full_unstemmed Tracking SARS-CoV-2 Variants Using a Rapid Typification Strategy: A Key Tool for Early Detection and Spread Investigation of Omicron in Argentina
title_short Tracking SARS-CoV-2 Variants Using a Rapid Typification Strategy: A Key Tool for Early Detection and Spread Investigation of Omicron in Argentina
title_sort tracking sars-cov-2 variants using a rapid typification strategy: a key tool for early detection and spread investigation of omicron in argentina
topic Medicine
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9157384/
https://www.ncbi.nlm.nih.gov/pubmed/35665324
http://dx.doi.org/10.3389/fmed.2022.851861
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