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.
Bibliographical noteFunding Information:
This work would not have been possible without the Danish COVID-19 Genome Consortium (DCGC); a full list of contributing consortium members can be found in Additional file 1. We gratefully acknowledge the Danish hospitals for local sequencing and data sharing. Thanks to all data contributors from outside Denmark, including the authors and their originating laboratories responsible for obtaining the specimens, as well as their submitting laboratories for generating the genetic sequence and metadata and sharing it via the GISAID Initiative. A full acknowledgement table is provided in Additional file 2. We would like to acknowledge the people at Data Integration and Analysis (DIAS), Statens Serum Institute, for managing and maintaining the national MiBa database which much of this work is based on. Thanks to the people at the Danish Patient Safety Authority for providing us with detailed travel records of SARS-CoV-2 positive cases. Thanks to Anna Zhukova, Institut Pasteur for modifying the pastML software to better fit our needs upon request. Finally, sincere thanks to Edyth Parker, Scripps Research, for insightful phylogenetic discussions.
© 2022, The Author(s).
ASJC Scopus subject areas
- Molecular Medicine
- Molecular Biology