High-resolution epidemiological landscape from  ~290,000 SARS-CoV-2 genomes from Denmark

Vast amounts of pathogen genomic, demographic and spatial data are transforming our understanding of SARS-CoV-2 emergence and spread. We examined the drivers of molecular evolution and spread of 291,791 SARS-CoV-2 genomes from Denmark in 2021. With a sequencing rate consistently exceeding 60%, and up to 80% of PCR-positive samples between March and November, the viral genome set is broadly whole-epidemic representative. We identify a consistent rise in viral diversity over time, with notable spikes upon the importation of novel variants (e.g., Delta and Omicron). By linking genomic data with rich individual-level demographic data from national registers, we find that individuals aged < 15 and > 75 years had a lower contribution to molecular change (i.e., branch lengths) compared to other age groups, but similar molecular evolutionary rates, suggesting a lower likelihood of introducing novel variants. Similarly, we find greater molecular change among vaccinated individuals, suggestive of immune evasion. We also observe evidence of transmission in rural areas to follow predictable diffusion processes. Conversely, urban areas are expectedly more complex due to their high mobility, emphasising the role of population structure in driving virus spread. Our analyses highlight the added value of integrating genomic data with detailed demographic and spatial information, particularly in the absence of structured infection surveys.

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Publication Details

Journal
Nature Communications
Published
2024-08-20
DOI
https://doi.org/10.1038/s41467-024-51371-0
Citations
6
Primary Topic
SARS-CoV-2 and COVID-19 Research
Type
article
Field-Weighted Citation Impact
2.33

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article

High-resolution epidemiological landscape from  ~290,000 SARS-CoV-2 genomes from Denmark

Man‐Hung Eric Tang, Raphael Niklaus Sieber, Louis du Plessis, Laust Hvas Mortensen et al.
6 citations
Nature Communications
SARS-CoV-2 and COVID-19 Research
2.33
article

High-resolution epidemiological landscape from  ~290,000 SARS-CoV-2 genomes from Denmark

Man‐Hung Eric Tang, Raphael Niklaus Sieber, Louis du Plessis, Laust Hvas Mortensen, Emil A. Sørensen, Morten Hoppe, John Coia, Jannik Fonager, Sune Lehmann, Henrik Ullum, Thomas Bygh Nymann Jensen, Tobias Gress, Christian Morgenstern, David Alejandro Duchêne, Dorte Terp Andersen, Marc Stegger, Marianne Nielsine Skov, Celine Petersen, Mark P. Khurana, Jonas L. Juul, Martin Schou Pedersen, Xiaohui Chen Nielsen, Pikka Jokelainen, Lene Nielsen, Jacob Curran-Sebastian, Thomas Yssing Michaelsen, Mads Albertsen, Morten Rasmussen, Kristian Schønning, Kirsten Ellegaard, Henrik Krarup, Moritz U. G. Kraemer, Neil Scheidwasser, Vithiagaran Gunalan, Gitte Nygaard Aasbjerg, Claus Henrik Nielsen, Tyra Grove Krause, Clarisse Chiche-Lapierre, Kasper Skytte Andersen, Nicolai Balle Larsen, José Alfredo Samaniego Castruita, Frederik Trier Møller, Rikke Lykke Johansen, Svend Ellermann‐Eriksen, Sanne Løkkegaard Larsen, Leandro Andrés Escobar-Herrera, Anders Møller Jensen, Thomas Sundelin, Kat Steinke, Stine Karstenskov Østergaard, Sarah Juel Paulsen, Marianne Kragh Thomsen, Susan Hove Hansen, Karina Gravgaard Thomsen, Samir Bhatt, Uffe Vest Schneider, Esben Mørk Hartmann, Emilio Fuster-Collados, Asta Lili Laugesen, Karina Meden Sørensen, Aleksander Ring, Jonas Byberg-Grauholm
article en
6 citations

Abstract

Vast amounts of pathogen genomic, demographic and spatial data are transforming our understanding of SARS-CoV-2 emergence and spread. We examined the drivers of molecular evolution and spread of 291,791 SARS-CoV-2 genomes from Denmark in 2021. With a sequencing rate consistently exceeding 60%, and up to 80% of PCR-positive samples between March and November, the viral genome set is broadly whole-epidemic representative. We identify a consistent rise in viral diversity over time, with notable spikes upon the importation of novel variants (e.g., Delta and Omicron). By linking genomic data with rich individual-level demographic data from national registers, we find that individuals aged < 15 and > 75 years had a lower contribution to molecular change (i.e., branch lengths) compared to other age groups, but similar molecular evolutionary rates, suggesting a lower likelihood of introducing novel variants. Similarly, we find greater molecular change among vaccinated individuals, suggestive of immune evasion. We also observe evidence of transmission in rural areas to follow predictable diffusion processes. Conversely, urban areas are expectedly more complex due to their high mobility, emphasising the role of population structure in driving virus spread. Our analyses highlight the added value of integrating genomic data with detailed demographic and spatial information, particularly in the absence of structured infection surveys.

Nature CommunicationsVol. 15(1)
Statens Serum Institut (DK), University of Copenhagen (DK), Statistics Denmark (DK), Murdoch University (AU), University of Southern Denmark (DK), Aalborg University Hospital (DK), Odense University Hospital (DK), Herlev Hospital (DK), Hvidovre Hospital (DK), Aarhus University Hospital (DK), Copenhagen University Hospital (DK), Rigshospitalet (DK), ETH Zurich (CH), University of Oxford (GB), Zealand University Hospital Køge (DK), Imperial College London (GB), Danmarks Nationalbank (DK), Aalborg University (DK), Technical University of Denmark (DK)
London School of Hygiene and Tropical Medicine, National Institute for Health Research Health Protection Research Unit, National Institute for Health and Care Research, Department of Health and Social Care, Imperial College London, National Research Foundation, Danmarks Grundforskningsfond, Novo Nordisk, Novo Nordisk Fonden, Medical Research Council, Statens Serum Institut, European and Developing Countries Clinical Trials Partnership
Good health and well-being
Openalex Percentile: Top 11%
SARS-CoV-2 and COVID-19 Research
2.33
DOIOpen Access PDFOpenAlex
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