High-resolution epidemiological landscape from ~290,000 SARS-CoV-2 genomes from Denmark
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High-resolution epidemiological landscape from ~290,000 SARS-CoV-2 genomes from Denmark. / Khurana, Mark P; Curran-Sebastian, Jacob; Scheidwasser, Neil; Morgenstern, Christian; Rasmussen, Morten; Fonager, Jannik; Stegger, Marc; Tang, Man-Hung Eric; Juul, Jonas L; Escobar-Herrera, Leandro Andrés; Møller, Frederik Trier; Albertsen, Mads; Kraemer, Moritz U G; du Plessis, Louis; Jokelainen, Pikka; Lehmann, Sune; Krause, Tyra G; Ullum, Henrik; Duchêne, David A; Mortensen, Laust H; Bhatt, Samir; Danish COVID-19 Genome Consortium (DCGC).
In: Nature Communications, Vol. 15, No. 1, 2024, p. 7123.Research output: Contribution to journal › Journal article › Research › peer-review
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TY - JOUR
T1 - High-resolution epidemiological landscape from ~290,000 SARS-CoV-2 genomes from Denmark
AU - Khurana, Mark P
AU - Curran-Sebastian, Jacob
AU - Scheidwasser, Neil
AU - Morgenstern, Christian
AU - Rasmussen, Morten
AU - Fonager, Jannik
AU - Stegger, Marc
AU - Tang, Man-Hung Eric
AU - Juul, Jonas L
AU - Escobar-Herrera, Leandro Andrés
AU - Møller, Frederik Trier
AU - Albertsen, Mads
AU - Kraemer, Moritz U G
AU - du Plessis, Louis
AU - Jokelainen, Pikka
AU - Lehmann, Sune
AU - Krause, Tyra G
AU - Ullum, Henrik
AU - Duchêne, David A
AU - Mortensen, Laust H
AU - Bhatt, Samir
AU - Danish COVID-19 Genome Consortium (DCGC)
N1 - © 2024. The Author(s).
PY - 2024
Y1 - 2024
N2 - 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.
AB - 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.
KW - Humans
KW - Denmark/epidemiology
KW - COVID-19/epidemiology
KW - SARS-CoV-2/genetics
KW - Genome, Viral/genetics
KW - Adult
KW - Middle Aged
KW - Aged
KW - Adolescent
KW - Young Adult
KW - Evolution, Molecular
KW - Male
KW - Female
KW - Child, Preschool
KW - Child
KW - Phylogeny
KW - Infant
U2 - 10.1038/s41467-024-51371-0
DO - 10.1038/s41467-024-51371-0
M3 - Journal article
C2 - 39164246
VL - 15
SP - 7123
JO - Nature Communications
JF - Nature Communications
SN - 2041-1723
IS - 1
ER -
ID: 403025036