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Journal article
High-resolution epidemiological landscape from ~290,000 SARS-CoV-2 genomes from Denmark
Nature communications, Vol.15(1), 7123
2024
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.
A high proportion of confirmed SARS-CoV-2 cases in Denmark were sequenced during the pandemic and linked to demographic, spatial and temporal data. Here, the authors analyse 290,000 genomes sampled in 2021 to demonstrate the value of this high coverage, detailed data set.
Details
- Title
- High-resolution epidemiological landscape from ~290,000 SARS-CoV-2 genomes from Denmark
- Authors/Creators
- Mark P. Khurana - University of CopenhagenJacob Curran-Sebastian - University of CopenhagenNeil Scheidwasser - Copenhagen, DenmarkChristian Morgenstern - Imperial College LondonMorten Rasmussen - Statens Serum InstitutJannik Fonager - Statens Serum InstitutMarc Stegger - Statens Serum InstitutMan-Hung Eric Tang - Statens Serum InstitutJonas L. Juul - Technical University of DenmarkLeandro Andrés Escobar-Herrera - Copenhagen, DenmarkFrederik Trier Møller - Statens Serum InstitutMads Albertsen - Aalborg UniversityMoritz U. G. Kraemer - University of OxfordLouis du Plessis - ETH ZurichPikka Jokelainen - Statens Serum InstitutSune Lehmann - Technical University of DenmarkTyra G. Krause - Copenhagen, DenmarkHenrik Ullum - Statens Serum InstitutDavid A. Duchêne - University of CopenhagenLaust H. Mortensen - Statistics DenmarkSamir Bhatt - Imperial College London
- Publication Details
- Nature communications, Vol.15(1), 7123
- Publisher
- Nature Publishing Group UK
- Identifiers
- 991005699170307891
- Copyright
- © The Author(s) 2024
- Murdoch Affiliation
- Murdoch University
- Language
- English
- Resource Type
- Journal article
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- Citation topics
- 1 Clinical & Life Sciences
- 1.104 Virology - General
- 1.104.1353 Coronavirus Research
- Web Of Science research areas
- Multidisciplinary Sciences
- ESI research areas
- Multidisciplinary