TY - JOUR
T1 - Introduction and transmission of SARS-CoV-2 lineage B.1.1.7, Alpha variant, in Denmark
AU - Michaelsen, Thomas Y
AU - Bennedbæk, Marc
AU - Christiansen, Lasse E
AU - Jørgensen, Mia S F
AU - Møller, Camilla H
AU - Sørensen, Emil A
AU - Knutsson, Simon
AU - Brandt, Jakob
AU - Jensen, Thomas B N
AU - Chiche-Lapierre, Clarisse
AU - Collados, Emilio F
AU - Sørensen, Trine
AU - Petersen, Celine
AU - Le-Quy, Vang
AU - Sereika, Mantas
AU - Hansen, Frederik T
AU - Rasmussen, Morten
AU - Fonager, Jannik
AU - Karst, Søren M
AU - Marvig, Rasmus L
AU - Stegger, Marc
AU - Sieber, Raphael N
AU - Skov, Robert
AU - Legarth, Rebecca
AU - Krause, Tyra G
AU - Fomsgaard, Anders
AU - Albertsen, Mads
AU - Danish COVID-19 Genome Consortium (DCGC)
N1 - © 2022. The Author(s).
PY - 2022/5/4
Y1 - 2022/5/4
N2 - 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.
AB - 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.
KW - COVID-19/epidemiology
KW - Denmark/epidemiology
KW - Humans
KW - Phylogeny
KW - SARS-CoV-2/genetics
UR - http://www.scopus.com/inward/record.url?scp=85129997318&partnerID=8YFLogxK
U2 - 10.1186/s13073-022-01045-7
DO - 10.1186/s13073-022-01045-7
M3 - Journal article
C2 - 35505393
SN - 1756-994X
VL - 14
SP - 1
EP - 13
JO - Genome Medicine
JF - Genome Medicine
IS - 1
M1 - 47
ER -