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Introduction and transmission of SARS-CoV-2 lineage B.1.1.7, Alpha variant, in Denmark

BACKGROUND: In early 2021, the SARS-CoV-2 lineage B.1.1.7 (Alpha variant) became dominant across large parts of the world. In Denmark, comprehensive and real-time test, contact-tracing, and sequencing efforts were applied to sustain epidemic control. Here, we use these data to investigate the transm...

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Autores principales: Michaelsen, Thomas Y., Bennedbæk, Marc, Christiansen, Lasse E., Jørgensen, Mia S. F., Møller, Camilla H., Sørensen, Emil A., Knutsson, Simon, Brandt, Jakob, Jensen, Thomas B. N., Chiche-Lapierre, Clarisse, Collados, Emilio F., Sørensen, Trine, Petersen, Celine, Le-Quy, Vang, Sereika, Mantas, Hansen, Frederik T., Rasmussen, Morten, Fonager, Jannik, Karst, Søren M., Marvig, Rasmus L., Stegger, Marc, Sieber, Raphael N., Skov, Robert, Legarth, Rebecca, Krause, Tyra G., Fomsgaard, Anders, Albertsen, Mads
Formato: Online Artículo Texto
Lenguaje:English
Publicado: BioMed Central 2022
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9064402/
https://www.ncbi.nlm.nih.gov/pubmed/35505393
http://dx.doi.org/10.1186/s13073-022-01045-7
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author Michaelsen, Thomas Y.
Bennedbæk, Marc
Christiansen, Lasse E.
Jørgensen, Mia S. F.
Møller, Camilla H.
Sørensen, Emil A.
Knutsson, Simon
Brandt, Jakob
Jensen, Thomas B. N.
Chiche-Lapierre, Clarisse
Collados, Emilio F.
Sørensen, Trine
Petersen, Celine
Le-Quy, Vang
Sereika, Mantas
Hansen, Frederik T.
Rasmussen, Morten
Fonager, Jannik
Karst, Søren M.
Marvig, Rasmus L.
Stegger, Marc
Sieber, Raphael N.
Skov, Robert
Legarth, Rebecca
Krause, Tyra G.
Fomsgaard, Anders
Albertsen, Mads
author_facet Michaelsen, Thomas Y.
Bennedbæk, Marc
Christiansen, Lasse E.
Jørgensen, Mia S. F.
Møller, Camilla H.
Sørensen, Emil A.
Knutsson, Simon
Brandt, Jakob
Jensen, Thomas B. N.
Chiche-Lapierre, Clarisse
Collados, Emilio F.
Sørensen, Trine
Petersen, Celine
Le-Quy, Vang
Sereika, Mantas
Hansen, Frederik T.
Rasmussen, Morten
Fonager, Jannik
Karst, Søren M.
Marvig, Rasmus L.
Stegger, Marc
Sieber, Raphael N.
Skov, Robert
Legarth, Rebecca
Krause, Tyra G.
Fomsgaard, Anders
Albertsen, Mads
author_sort Michaelsen, Thomas Y.
collection PubMed
description BACKGROUND: In early 2021, the SARS-CoV-2 lineage B.1.1.7 (Alpha variant) became dominant across large parts of the world. In Denmark, comprehensive and real-time test, contact-tracing, and sequencing efforts were applied to sustain epidemic control. Here, we use these data to investigate the transmissibility, introduction, and onward transmission of B.1.1.7 in Denmark. METHODS: We analyzed a comprehensive set of 60,178 SARS-CoV-2 genomes generated from high-throughput sequencing by the Danish COVID-19 Genome Consortium, representing 34% of all positive cases in the period 14 November 2020 to 7 February 2021. We calculated the transmissibility of B.1.1.7 relative to other lineages using Poisson regression. Including all 1976 high-quality B.1.1.7 genomes collected in the study period, we constructed a time-scaled phylogeny, which was coupled with detailed travel history and register data to outline the introduction and onward transmission of B.1.1.7 in Denmark. RESULTS: In a period with unchanged restrictions, we estimated an increased B.1.1.7 transmissibility of 58% (95% CI: [56%, 60%]) relative to other lineages. Epidemiological and phylogenetic analyses revealed that 37% of B.1.1.7 cases were related to the initial introduction in November 2020. The relative number of cases directly linked to introductions varied between 10 and 50% throughout the study period. CONCLUSIONS: Our findings corroborate early estimates of increased transmissibility of B.1.1.7. Both substantial early expansion when B.1.1.7 was still unmonitored and continuous foreign introductions contributed considerably to case numbers. Finally, our study highlights the benefit of balanced travel restrictions and self-isolation procedures coupled with comprehensive surveillance efforts, to sustain epidemic control in the face of emerging variants. SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s13073-022-01045-7.
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spelling pubmed-90644022022-05-04 Introduction and transmission of SARS-CoV-2 lineage B.1.1.7, Alpha variant, in Denmark Michaelsen, Thomas Y. Bennedbæk, Marc Christiansen, Lasse E. Jørgensen, Mia S. F. Møller, Camilla H. Sørensen, Emil A. Knutsson, Simon Brandt, Jakob Jensen, Thomas B. N. Chiche-Lapierre, Clarisse Collados, Emilio F. Sørensen, Trine Petersen, Celine Le-Quy, Vang Sereika, Mantas Hansen, Frederik T. Rasmussen, Morten Fonager, Jannik Karst, Søren M. Marvig, Rasmus L. Stegger, Marc Sieber, Raphael N. Skov, Robert Legarth, Rebecca Krause, Tyra G. Fomsgaard, Anders Albertsen, Mads Genome Med Research BACKGROUND: In early 2021, the SARS-CoV-2 lineage B.1.1.7 (Alpha variant) became dominant across large parts of the world. In Denmark, comprehensive and real-time test, contact-tracing, and sequencing efforts were applied to sustain epidemic control. Here, we use these data to investigate the transmissibility, introduction, and onward transmission of B.1.1.7 in Denmark. METHODS: We analyzed a comprehensive set of 60,178 SARS-CoV-2 genomes generated from high-throughput sequencing by the Danish COVID-19 Genome Consortium, representing 34% of all positive cases in the period 14 November 2020 to 7 February 2021. We calculated the transmissibility of B.1.1.7 relative to other lineages using Poisson regression. Including all 1976 high-quality B.1.1.7 genomes collected in the study period, we constructed a time-scaled phylogeny, which was coupled with detailed travel history and register data to outline the introduction and onward transmission of B.1.1.7 in Denmark. RESULTS: In a period with unchanged restrictions, we estimated an increased B.1.1.7 transmissibility of 58% (95% CI: [56%, 60%]) relative to other lineages. Epidemiological and phylogenetic analyses revealed that 37% of B.1.1.7 cases were related to the initial introduction in November 2020. The relative number of cases directly linked to introductions varied between 10 and 50% throughout the study period. CONCLUSIONS: Our findings corroborate early estimates of increased transmissibility of B.1.1.7. Both substantial early expansion when B.1.1.7 was still unmonitored and continuous foreign introductions contributed considerably to case numbers. Finally, our study highlights the benefit of balanced travel restrictions and self-isolation procedures coupled with comprehensive surveillance efforts, to sustain epidemic control in the face of emerging variants. SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s13073-022-01045-7. BioMed Central 2022-05-04 /pmc/articles/PMC9064402/ /pubmed/35505393 http://dx.doi.org/10.1186/s13073-022-01045-7 Text en © The Author(s) 2022 https://creativecommons.org/licenses/by/4.0/Open AccessThis 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, visithttp://creativecommons.org/licenses/by/4.0/ (https://creativecommons.org/licenses/by/4.0/) . The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/ (https://creativecommons.org/publicdomain/zero/1.0/) ) applies to the data made available in this article, unless otherwise stated in a credit line to the data.
spellingShingle Research
Michaelsen, Thomas Y.
Bennedbæk, Marc
Christiansen, Lasse E.
Jørgensen, Mia S. F.
Møller, Camilla H.
Sørensen, Emil A.
Knutsson, Simon
Brandt, Jakob
Jensen, Thomas B. N.
Chiche-Lapierre, Clarisse
Collados, Emilio F.
Sørensen, Trine
Petersen, Celine
Le-Quy, Vang
Sereika, Mantas
Hansen, Frederik T.
Rasmussen, Morten
Fonager, Jannik
Karst, Søren M.
Marvig, Rasmus L.
Stegger, Marc
Sieber, Raphael N.
Skov, Robert
Legarth, Rebecca
Krause, Tyra G.
Fomsgaard, Anders
Albertsen, Mads
Introduction and transmission of SARS-CoV-2 lineage B.1.1.7, Alpha variant, in Denmark
title Introduction and transmission of SARS-CoV-2 lineage B.1.1.7, Alpha variant, in Denmark
title_full Introduction and transmission of SARS-CoV-2 lineage B.1.1.7, Alpha variant, in Denmark
title_fullStr Introduction and transmission of SARS-CoV-2 lineage B.1.1.7, Alpha variant, in Denmark
title_full_unstemmed Introduction and transmission of SARS-CoV-2 lineage B.1.1.7, Alpha variant, in Denmark
title_short Introduction and transmission of SARS-CoV-2 lineage B.1.1.7, Alpha variant, in Denmark
title_sort introduction and transmission of sars-cov-2 lineage b.1.1.7, alpha variant, in denmark
topic Research
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9064402/
https://www.ncbi.nlm.nih.gov/pubmed/35505393
http://dx.doi.org/10.1186/s13073-022-01045-7
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