Molecular epidemiology of the SARS-CoV-2 variant Omicron BA.2 sub-lineage in Denmark, 29 November 2021 to 2 January 2022

Jannik Fonager; Marc Bennedbæk; Peter Bager; Jan Wohlfahrt; Kirsten Maren Ellegaard; Anna Cäcilia Ingham; Sofie Marie Edslev; Marc Stegger; Raphael Niklaus Sieber; Ria Lassauniere; Anders Fomsgaard; Troels Lillebaek; Christina Wiid Svarrer; Frederik Trier Møller; Camilla Holten Møller; Rebecca Legarth; Thomas Vognbjerg Sydenham; Kat Steinke; Sarah Juel Paulsen; José Alfredo Samaniego Castruita; Uffe Vest Schneider; Christian Højte Schouw; Xiaohui Chen Nielsen; Maria Overvad; Rikke Thoft Nielsen; Rasmus L Marvig; Martin Schou Pedersen; Lene Nielsen; Line Lynge Nilsson; Jonas Bybjerg-Grauholm; Irene Harder Tarpgaard; Tine Snejbjerg Ebsen; Janni Uyen Hoa Lam; Vithiagaran Gunalan; Morten Rasmussen

doi:10.2807/1560-7917.ES.2022.27.10.2200181

Molecular epidemiology of the SARS-CoV-2 variant Omicron BA.2 sub-lineage in Denmark, 29 November 2021 to 2 January 2022

Jannik Fonager^*, Marc Bennedbæk, Peter Bager, Jan Wohlfahrt, Kirsten Maren Ellegaard, Anna Cäcilia Ingham, Sofie Marie Edslev, Marc Stegger, Raphael Niklaus Sieber, Ria Lassauniere, Anders Fomsgaard, Troels Lillebaek, Christina Wiid Svarrer, Frederik Trier Møller, Camilla Holten Møller, Rebecca Legarth, Thomas Vognbjerg Sydenham, Kat Steinke, Sarah Juel Paulsen, José Alfredo Samaniego CastruitaUffe Vest Schneider, Christian Højte Schouw, Xiaohui Chen Nielsen, Maria Overvad, Rikke Thoft Nielsen, Rasmus L Marvig, Martin Schou Pedersen, Lene Nielsen, Line Lynge Nilsson, Jonas Bybjerg-Grauholm, Irene Harder Tarpgaard, Tine Snejbjerg Ebsen, Janni Uyen Hoa Lam, Vithiagaran Gunalan, Morten Rasmussen

^*Corresponding author for this work

67 Citations (Scopus)

Abstract

Following emergence of the SARS-CoV-2 variant Omicron in November 2021, the dominant BA.1 sub-lineage was replaced by the BA.2 sub-lineage in Denmark. We analysed the first 2,623 BA.2 cases from 29 November 2021 to 2 January 2022. No epidemiological or clinical differences were found between individuals infected with BA.1 versus BA.2. Phylogenetic analyses showed a geographic east-to-west transmission of BA.2 from the Capital Region with clusters expanding after the Christmas holidays. Mutational analysis shows distinct differences between BA.1 and BA.2.

Original language	English
Journal	Eurosurveillance
Volume	27
Issue number	10
Pages (from-to)	1-7
Number of pages	7
ISSN	1560-7917
DOIs	https://doi.org/10.2807/1560-7917.ES.2022.27.10.2200181
Publication status	Published - 10 Mar 2022

Keywords

COVID-19/epidemiology
Denmark/epidemiology
Humans
Molecular Epidemiology
Phylogeny
SARS-CoV-2/genetics
COVID-19
SARS-CoV-2
variant of concern
Omicron
BA.1
BA.2

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Fonager, J., Bennedbæk, M., Bager, P., Wohlfahrt, J., Ellegaard, K. M., Ingham, A. C., Edslev, S. M., Stegger, M., Sieber, R. N., Lassauniere, R., Fomsgaard, A., Lillebaek, T., Svarrer, C. W., Møller, F. T., Møller, C. H., Legarth, R., Sydenham, T. V., Steinke, K., Paulsen, S. J., ... Rasmussen, M. (2022). Molecular epidemiology of the SARS-CoV-2 variant Omicron BA.2 sub-lineage in Denmark, 29 November 2021 to 2 January 2022. Eurosurveillance, 27(10), 1-7. https://doi.org/10.2807/1560-7917.ES.2022.27.10.2200181

Fonager, J, Bennedbæk, M, Bager, P, Wohlfahrt, J, Ellegaard, KM, Ingham, AC, Edslev, SM, Stegger, M, Sieber, RN, Lassauniere, R, Fomsgaard, A, Lillebaek, T, Svarrer, CW, Møller, FT, Møller, CH, Legarth, R, Sydenham, TV, Steinke, K, Paulsen, SJ, Castruita, JAS, Schneider, UV, Schouw, CH, Nielsen, XC, Overvad, M, Nielsen, RT, Marvig, RL , Pedersen, MS , Nielsen, L, Nilsson, LL, Bybjerg-Grauholm, J, Tarpgaard, IH, Ebsen, TS, Lam, JUH, Gunalan, V & Rasmussen, M 2022, 'Molecular epidemiology of the SARS-CoV-2 variant Omicron BA.2 sub-lineage in Denmark, 29 November 2021 to 2 January 2022', Eurosurveillance, vol. 27, no. 10, pp. 1-7. https://doi.org/10.2807/1560-7917.ES.2022.27.10.2200181

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title = "Molecular epidemiology of the SARS-CoV-2 variant Omicron BA.2 sub-lineage in Denmark, 29 November 2021 to 2 January 2022",

abstract = "Following emergence of the SARS-CoV-2 variant Omicron in November 2021, the dominant BA.1 sub-lineage was replaced by the BA.2 sub-lineage in Denmark. We analysed the first 2,623 BA.2 cases from 29 November 2021 to 2 January 2022. No epidemiological or clinical differences were found between individuals infected with BA.1 versus BA.2. Phylogenetic analyses showed a geographic east-to-west transmission of BA.2 from the Capital Region with clusters expanding after the Christmas holidays. Mutational analysis shows distinct differences between BA.1 and BA.2.",

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AU - Fonager, Jannik

AU - Bennedbæk, Marc

AU - Bager, Peter

AU - Wohlfahrt, Jan

AU - Ellegaard, Kirsten Maren

AU - Ingham, Anna Cäcilia

AU - Edslev, Sofie Marie

AU - Stegger, Marc

AU - Sieber, Raphael Niklaus

AU - Lassauniere, Ria

AU - Fomsgaard, Anders

AU - Lillebaek, Troels

AU - Svarrer, Christina Wiid

AU - Møller, Frederik Trier

AU - Møller, Camilla Holten

AU - Legarth, Rebecca

AU - Sydenham, Thomas Vognbjerg

AU - Steinke, Kat

AU - Paulsen, Sarah Juel

AU - Castruita, José Alfredo Samaniego

AU - Schneider, Uffe Vest

AU - Schouw, Christian Højte

AU - Nielsen, Xiaohui Chen

AU - Overvad, Maria

AU - Nielsen, Rikke Thoft

AU - Marvig, Rasmus L

AU - Pedersen, Martin Schou

AU - Nielsen, Lene

AU - Nilsson, Line Lynge

AU - Bybjerg-Grauholm, Jonas

AU - Tarpgaard, Irene Harder

AU - Ebsen, Tine Snejbjerg

AU - Lam, Janni Uyen Hoa

AU - Gunalan, Vithiagaran

AU - Rasmussen, Morten

PY - 2022/3/10

Y1 - 2022/3/10

N2 - Following emergence of the SARS-CoV-2 variant Omicron in November 2021, the dominant BA.1 sub-lineage was replaced by the BA.2 sub-lineage in Denmark. We analysed the first 2,623 BA.2 cases from 29 November 2021 to 2 January 2022. No epidemiological or clinical differences were found between individuals infected with BA.1 versus BA.2. Phylogenetic analyses showed a geographic east-to-west transmission of BA.2 from the Capital Region with clusters expanding after the Christmas holidays. Mutational analysis shows distinct differences between BA.1 and BA.2.

AB - Following emergence of the SARS-CoV-2 variant Omicron in November 2021, the dominant BA.1 sub-lineage was replaced by the BA.2 sub-lineage in Denmark. We analysed the first 2,623 BA.2 cases from 29 November 2021 to 2 January 2022. No epidemiological or clinical differences were found between individuals infected with BA.1 versus BA.2. Phylogenetic analyses showed a geographic east-to-west transmission of BA.2 from the Capital Region with clusters expanding after the Christmas holidays. Mutational analysis shows distinct differences between BA.1 and BA.2.

KW - COVID-19/epidemiology

KW - Denmark/epidemiology

KW - Humans

KW - Molecular Epidemiology

KW - Phylogeny

KW - SARS-CoV-2/genetics

KW - COVID-19

KW - SARS-CoV-2

KW - variant of concern

KW - Omicron

KW - BA.1

KW - BA.2

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U2 - 10.2807/1560-7917.ES.2022.27.10.2200181

DO - 10.2807/1560-7917.ES.2022.27.10.2200181

M3 - Journal article

C2 - 35272746

SN - 1560-7917

VL - 27

SP - 1

EP - 7

JO - Eurosurveillance

JF - Eurosurveillance

IS - 10

ER -

Molecular epidemiology of the SARS-CoV-2 variant Omicron BA.2 sub-lineage in Denmark, 29 November 2021 to 2 January 2022

Abstract

Keywords

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