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Monitoring SARS-CoV-2 variant transitions using differences in diagnostic cycle threshold values of target genes

Monitoring the emergence of new SARS-CoV-2 variants is important to detect potential risks of increased transmission or disease severity. We investigated the identification of SARS-CoV-2 variants from real-time reverse transcriptase polymerase chain reaction (RT-PCR) routine diagnostics data. Cycle...

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Autores principales: Bordoy, Antoni E., Saludes, Verónica, Panisello Yagüe, David, Clarà, Gemma, Soler, Laia, Paris de León, Alexia, Casañ, Cristina, Blanco-Suárez, Ana, Guerrero-Murillo, Mercedes, Rodríguez-Ponga, Beatriz, Noguera-Julian, Marc, Català-Moll, Francesc, Pey, Irina, Armengol, Maria Pilar, Casadellà, Maria, Parera, Mariona, Pluvinet, Raquel, Sumoy, Lauro, Clotet, Bonaventura, Giménez, Montserrat, Martró, Elisa, Cardona, Pere-Joan, Blanco, Ignacio
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Nature Publishing Group UK 2022
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9758454/
https://www.ncbi.nlm.nih.gov/pubmed/36528712
http://dx.doi.org/10.1038/s41598-022-25719-9
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author Bordoy, Antoni E.
Saludes, Verónica
Panisello Yagüe, David
Clarà, Gemma
Soler, Laia
Paris de León, Alexia
Casañ, Cristina
Blanco-Suárez, Ana
Guerrero-Murillo, Mercedes
Rodríguez-Ponga, Beatriz
Noguera-Julian, Marc
Català-Moll, Francesc
Pey, Irina
Armengol, Maria Pilar
Casadellà, Maria
Parera, Mariona
Pluvinet, Raquel
Sumoy, Lauro
Clotet, Bonaventura
Giménez, Montserrat
Martró, Elisa
Cardona, Pere-Joan
Blanco, Ignacio
author_facet Bordoy, Antoni E.
Saludes, Verónica
Panisello Yagüe, David
Clarà, Gemma
Soler, Laia
Paris de León, Alexia
Casañ, Cristina
Blanco-Suárez, Ana
Guerrero-Murillo, Mercedes
Rodríguez-Ponga, Beatriz
Noguera-Julian, Marc
Català-Moll, Francesc
Pey, Irina
Armengol, Maria Pilar
Casadellà, Maria
Parera, Mariona
Pluvinet, Raquel
Sumoy, Lauro
Clotet, Bonaventura
Giménez, Montserrat
Martró, Elisa
Cardona, Pere-Joan
Blanco, Ignacio
author_sort Bordoy, Antoni E.
collection PubMed
description Monitoring the emergence of new SARS-CoV-2 variants is important to detect potential risks of increased transmission or disease severity. We investigated the identification of SARS-CoV-2 variants from real-time reverse transcriptase polymerase chain reaction (RT-PCR) routine diagnostics data. Cycle threshold (Ct) values of positive samples were collected from April 2021 to January 2022 in the Northern Metropolitan Area of Barcelona (n = 15,254). Viral lineage identification from whole genome sequencing (WGS) was available for 4618 (30.3%) of these samples. Pairwise differences in the Ct values between gene targets (ΔCt) were analyzed for variants of concern or interest circulating in our area. A specific delay in the Ct of the N-gene compared to the RdRp-gene (ΔCt(NR)) was observed for Alpha, Delta, Eta and Omicron. Temporal differences in ΔCt(NR) correlated with the dynamics of viral replacement of Alpha by Delta and of Delta by Omicron according to WGS results. Using ΔCt(NR), prediction of new variants of concern at early stages of circulation was achieved with high sensitivity and specificity (91.1% and 97.8% for Delta; 98.5% and 90.8% for Omicron). Thus, tracking population-wide trends in ΔCt values obtained from routine diagnostics testing in combination with WGS could be useful for real-time management and response to local epidemics.
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spelling pubmed-97584542022-12-19 Monitoring SARS-CoV-2 variant transitions using differences in diagnostic cycle threshold values of target genes Bordoy, Antoni E. Saludes, Verónica Panisello Yagüe, David Clarà, Gemma Soler, Laia Paris de León, Alexia Casañ, Cristina Blanco-Suárez, Ana Guerrero-Murillo, Mercedes Rodríguez-Ponga, Beatriz Noguera-Julian, Marc Català-Moll, Francesc Pey, Irina Armengol, Maria Pilar Casadellà, Maria Parera, Mariona Pluvinet, Raquel Sumoy, Lauro Clotet, Bonaventura Giménez, Montserrat Martró, Elisa Cardona, Pere-Joan Blanco, Ignacio Sci Rep Article Monitoring the emergence of new SARS-CoV-2 variants is important to detect potential risks of increased transmission or disease severity. We investigated the identification of SARS-CoV-2 variants from real-time reverse transcriptase polymerase chain reaction (RT-PCR) routine diagnostics data. Cycle threshold (Ct) values of positive samples were collected from April 2021 to January 2022 in the Northern Metropolitan Area of Barcelona (n = 15,254). Viral lineage identification from whole genome sequencing (WGS) was available for 4618 (30.3%) of these samples. Pairwise differences in the Ct values between gene targets (ΔCt) were analyzed for variants of concern or interest circulating in our area. A specific delay in the Ct of the N-gene compared to the RdRp-gene (ΔCt(NR)) was observed for Alpha, Delta, Eta and Omicron. Temporal differences in ΔCt(NR) correlated with the dynamics of viral replacement of Alpha by Delta and of Delta by Omicron according to WGS results. Using ΔCt(NR), prediction of new variants of concern at early stages of circulation was achieved with high sensitivity and specificity (91.1% and 97.8% for Delta; 98.5% and 90.8% for Omicron). Thus, tracking population-wide trends in ΔCt values obtained from routine diagnostics testing in combination with WGS could be useful for real-time management and response to local epidemics. Nature Publishing Group UK 2022-12-17 /pmc/articles/PMC9758454/ /pubmed/36528712 http://dx.doi.org/10.1038/s41598-022-25719-9 Text en © The Author(s) 2022 https://creativecommons.org/licenses/by/4.0/Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons licence, and indicate if changes were made. The images or other third party material in this article are included in the article's Creative Commons licence, unless indicated otherwise in a credit line to the material. If material is not included in the article's Creative Commons licence and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this licence, visit http://creativecommons.org/licenses/by/4.0/ (https://creativecommons.org/licenses/by/4.0/) .
spellingShingle Article
Bordoy, Antoni E.
Saludes, Verónica
Panisello Yagüe, David
Clarà, Gemma
Soler, Laia
Paris de León, Alexia
Casañ, Cristina
Blanco-Suárez, Ana
Guerrero-Murillo, Mercedes
Rodríguez-Ponga, Beatriz
Noguera-Julian, Marc
Català-Moll, Francesc
Pey, Irina
Armengol, Maria Pilar
Casadellà, Maria
Parera, Mariona
Pluvinet, Raquel
Sumoy, Lauro
Clotet, Bonaventura
Giménez, Montserrat
Martró, Elisa
Cardona, Pere-Joan
Blanco, Ignacio
Monitoring SARS-CoV-2 variant transitions using differences in diagnostic cycle threshold values of target genes
title Monitoring SARS-CoV-2 variant transitions using differences in diagnostic cycle threshold values of target genes
title_full Monitoring SARS-CoV-2 variant transitions using differences in diagnostic cycle threshold values of target genes
title_fullStr Monitoring SARS-CoV-2 variant transitions using differences in diagnostic cycle threshold values of target genes
title_full_unstemmed Monitoring SARS-CoV-2 variant transitions using differences in diagnostic cycle threshold values of target genes
title_short Monitoring SARS-CoV-2 variant transitions using differences in diagnostic cycle threshold values of target genes
title_sort monitoring sars-cov-2 variant transitions using differences in diagnostic cycle threshold values of target genes
topic Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9758454/
https://www.ncbi.nlm.nih.gov/pubmed/36528712
http://dx.doi.org/10.1038/s41598-022-25719-9
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