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Assessment of Mutations Associated With Genomic Variants of SARS-CoV-2: RT-qPCR as a Rapid and Affordable Tool to Monitoring Known Circulating Variants in Chile, 2021

Since the first report of SARS-CoV-2 infection in humans, the virus has mutated to develop new viral variants with higher infection rates and more resistance to neutralization by antibodies elicited after natural SARS-CoV-2 infection or by vaccines. Therefore, rapid identification of viral variants...

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Autores principales: Angulo, Jenniffer, Martinez-Valdebenito, Constanza, Pardo-Roa, Catalina, Almonacid, Leonardo I., Fuentes-Luppichini, Eugenia, Contreras, Ana Maria, Maldonado, Constanza, Le Corre, Nicole, Melo, Francisco, Medina, Rafael A., Ferrés, Marcela
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Frontiers Media S.A. 2022
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8914012/
https://www.ncbi.nlm.nih.gov/pubmed/35280916
http://dx.doi.org/10.3389/fmed.2022.841073
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author Angulo, Jenniffer
Martinez-Valdebenito, Constanza
Pardo-Roa, Catalina
Almonacid, Leonardo I.
Fuentes-Luppichini, Eugenia
Contreras, Ana Maria
Maldonado, Constanza
Le Corre, Nicole
Melo, Francisco
Medina, Rafael A.
Ferrés, Marcela
author_facet Angulo, Jenniffer
Martinez-Valdebenito, Constanza
Pardo-Roa, Catalina
Almonacid, Leonardo I.
Fuentes-Luppichini, Eugenia
Contreras, Ana Maria
Maldonado, Constanza
Le Corre, Nicole
Melo, Francisco
Medina, Rafael A.
Ferrés, Marcela
author_sort Angulo, Jenniffer
collection PubMed
description Since the first report of SARS-CoV-2 infection in humans, the virus has mutated to develop new viral variants with higher infection rates and more resistance to neutralization by antibodies elicited after natural SARS-CoV-2 infection or by vaccines. Therefore, rapid identification of viral variants circulating in the population is crucial for epidemiological assessment and efforts to contain the resurgence of the pandemic. Between January and November 2021, we performed a large variant RT-qPCR-based screening of mutations in the spike protein of 1851 SARS-CoV-2-positive samples derived from outpatients from the UC-Christus Health Network in Chile. In a portion of samples (n = 636), we validated our RT-qPCR-pipeline by WGS, obtaining a 99.2% concordance. Our results indicate that from January to March 2021 there was a dominance of non-identifiable variants by the RT-qPCR-based screening; however, throughout WGS we were able to identify the Lambda (C.37) variant of interest (VOI). From March to July, we observed the rapid emergence of mutations associated with the Gamma variant (P.1), which was quickly replaced by the appearance of a combination of samples harboring mutations associated with the Delta variant (B.1.617.2), which predominated until the end of the study. Our results highlight the applicability of cost-effective RT-qPCR-based screening of mutations associated with known variants of concern (VOC), VOI and variants under monitoring (VUM) of SARS-CoV-2, being a rapid and reliable tool that complements WGS-based surveillance.
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spelling pubmed-89140122022-03-12 Assessment of Mutations Associated With Genomic Variants of SARS-CoV-2: RT-qPCR as a Rapid and Affordable Tool to Monitoring Known Circulating Variants in Chile, 2021 Angulo, Jenniffer Martinez-Valdebenito, Constanza Pardo-Roa, Catalina Almonacid, Leonardo I. Fuentes-Luppichini, Eugenia Contreras, Ana Maria Maldonado, Constanza Le Corre, Nicole Melo, Francisco Medina, Rafael A. Ferrés, Marcela Front Med (Lausanne) Medicine Since the first report of SARS-CoV-2 infection in humans, the virus has mutated to develop new viral variants with higher infection rates and more resistance to neutralization by antibodies elicited after natural SARS-CoV-2 infection or by vaccines. Therefore, rapid identification of viral variants circulating in the population is crucial for epidemiological assessment and efforts to contain the resurgence of the pandemic. Between January and November 2021, we performed a large variant RT-qPCR-based screening of mutations in the spike protein of 1851 SARS-CoV-2-positive samples derived from outpatients from the UC-Christus Health Network in Chile. In a portion of samples (n = 636), we validated our RT-qPCR-pipeline by WGS, obtaining a 99.2% concordance. Our results indicate that from January to March 2021 there was a dominance of non-identifiable variants by the RT-qPCR-based screening; however, throughout WGS we were able to identify the Lambda (C.37) variant of interest (VOI). From March to July, we observed the rapid emergence of mutations associated with the Gamma variant (P.1), which was quickly replaced by the appearance of a combination of samples harboring mutations associated with the Delta variant (B.1.617.2), which predominated until the end of the study. Our results highlight the applicability of cost-effective RT-qPCR-based screening of mutations associated with known variants of concern (VOC), VOI and variants under monitoring (VUM) of SARS-CoV-2, being a rapid and reliable tool that complements WGS-based surveillance. Frontiers Media S.A. 2022-02-25 /pmc/articles/PMC8914012/ /pubmed/35280916 http://dx.doi.org/10.3389/fmed.2022.841073 Text en Copyright © 2022 Angulo, Martinez-Valdebenito, Pardo-Roa, Almonacid, Fuentes-Luppichini, Contreras, Maldonado, Le Corre, Melo, Medina and Ferrés. 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
Angulo, Jenniffer
Martinez-Valdebenito, Constanza
Pardo-Roa, Catalina
Almonacid, Leonardo I.
Fuentes-Luppichini, Eugenia
Contreras, Ana Maria
Maldonado, Constanza
Le Corre, Nicole
Melo, Francisco
Medina, Rafael A.
Ferrés, Marcela
Assessment of Mutations Associated With Genomic Variants of SARS-CoV-2: RT-qPCR as a Rapid and Affordable Tool to Monitoring Known Circulating Variants in Chile, 2021
title Assessment of Mutations Associated With Genomic Variants of SARS-CoV-2: RT-qPCR as a Rapid and Affordable Tool to Monitoring Known Circulating Variants in Chile, 2021
title_full Assessment of Mutations Associated With Genomic Variants of SARS-CoV-2: RT-qPCR as a Rapid and Affordable Tool to Monitoring Known Circulating Variants in Chile, 2021
title_fullStr Assessment of Mutations Associated With Genomic Variants of SARS-CoV-2: RT-qPCR as a Rapid and Affordable Tool to Monitoring Known Circulating Variants in Chile, 2021
title_full_unstemmed Assessment of Mutations Associated With Genomic Variants of SARS-CoV-2: RT-qPCR as a Rapid and Affordable Tool to Monitoring Known Circulating Variants in Chile, 2021
title_short Assessment of Mutations Associated With Genomic Variants of SARS-CoV-2: RT-qPCR as a Rapid and Affordable Tool to Monitoring Known Circulating Variants in Chile, 2021
title_sort assessment of mutations associated with genomic variants of sars-cov-2: rt-qpcr as a rapid and affordable tool to monitoring known circulating variants in chile, 2021
topic Medicine
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8914012/
https://www.ncbi.nlm.nih.gov/pubmed/35280916
http://dx.doi.org/10.3389/fmed.2022.841073
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