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 - The Danish COVID-19 Genome Consortium (DCGC)
AU - Chiche-Lapierre, Clarisse
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
A2 - Byberg-Grauholm, Jonas
A2 - Aasbjerg, Gitte Nygaard
A2 - Ring, Aleksander
A2 - Sieber, Raphael
A2 - Hansen, Tobias Nikolaj Gress
A2 - Gunalan, Vithiagaran
A2 - Nielsen, Claus
A2 - Ellegaard, Kirsten
A2 - Larsen, Nicolai Balle
A2 - Hartmann, Esben Mørk
A2 - Jensen, Anders
A2 - Sørensen, Karina Meden
A2 - Østergaard, Stine K.
A2 - Sørensen, Emil A.
A2 - Jensen, Thomas B. N.
A2 - Fuster-Collados, Emilio
A2 - Andersen, Kasper S.
A2 - Michaelsen, Thomas Y.
A2 - Petersen, Celine
A2 - Hansen, Susan H.
A2 - Krarup, Henrik Bygum
A2 - Schønning, Kristian
A2 - Paulsen, Sarah Juel
A2 - Schneider, Uffe Vest
A2 - Pedersen, Martin Schou
A2 - Castruita, Jose Alfredo Samaniego
A2 - Thomsen, Marianne Kragh
A2 - Ellermann-Eriksen, Svend
A2 - Thomsen, Karina Gravgaard
A2 - Steinke, Kat
A2 - Andersen, Dorte Terp
A2 - Skov, Marianne Nielsine
A2 - Larsen, Sanne Løkkegaard
A2 - Hoppe, Morten
A2 - Nielsen, Lene
A2 - Sundelin, Thomas
A2 - Coia, John E.
A2 - Laugesen, Asta Lili
A2 - Johansen, Rikke Lykke
A2 - Nielsen, Xiaohui
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.
UR - http://www.scopus.com/inward/record.url?scp=85201851941&partnerID=8YFLogxK
U2 - 10.1038/s41467-024-51371-0
DO - 10.1038/s41467-024-51371-0
M3 - Journal article
C2 - 39164246
SN - 2041-1723
VL - 15
JO - Nature Communications
JF - Nature Communications
M1 - 7123
ER -