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
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.