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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...
Autores principales: | , , , , , , , , , , , , , , , , , , , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
Nature Publishing Group UK
2022
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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. |
format | Online Article Text |
id | pubmed-9758454 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2022 |
publisher | Nature Publishing Group UK |
record_format | MEDLINE/PubMed |
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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