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 -