Introduction and transmission of SARS-CoV-2 lineage B.1.1.7, Alpha variant, in Denmark
Authors: 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 ,   The Danish COVID-19 Genome Consortium (DCGC), Andersen Kasper S. , Andersen Martin H. , Berg Amalie , Bielidt Susanne R. , Dall Sebastian M. , Dvarionaite Erika , Hansen Susan H. , Jørgensen Vibeke R. , Kirkegaard Rasmus H. , Saei Wagma , Nicolajsen Trine B. , Østergaard Stine K. , Brøndum Rasmus F. , Bøgsted Martin , Hose Katja , Sagi Tomer , Pakanec Miroslaw , Fuglsang-Damgaard David , Mølvadgaard Mette , Krarup Henrik , Svarrer Christina W. , Christiansen Mette T. , Ingham Anna C. , Johannesen Thor B. , Basterrechea Martín , Lilje Berit , Ellegaard Kirsten , Matusevicius Povilas , Christoffersen Lars B. , Tang Man-Hung E. , Ng Kim L. , Edslev Sofie M. , Baig Sharmin , Larsen Ole H. , Skipper Kristian A. , Vang Søren , Handberg Kurt J. , Nielsen Marc T. K. , Kobel Carl M. , Andersen Camilla , Tarpgaard Irene H. , Ellermann-Eriksen Svend , Castruita José A. S. , Schneider Uffe V. , Jacobsen Nana G. , Andersen Christian Ø. , Pedersen Martin S. , Schønning Kristian , Kirkby Nikolai , Nielsen Lene , Nilsson Line L. , Friis Martin B. , Sundelin Thomas , Hansen Thomas A. , Skov Marianne N. , Sydenham Thomas V. , Nielsen Xiaohui C. , Schouw Christian H. , Jensen Anders , Marmolin Ea S. , Coia John E. , Andersen Dorte T. , Albertsen Mads 
Published: May 2022

Abstract
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.