TY - JOUR
T1 - High-resolution epidemiological landscape from textasciitilde290,000 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 - (dcgc), The Danish COVID-19 Genome Consortium
AU - Byberg-Grauholm, Jonas
AU - Aasbjerg, Gitte Nygaard
AU - Ring, Aleksander
AU - Sieber, Raphael
AU - Hansen, Tobias Nikolaj Gress
AU - Gunalan, Vithiagaran
AU - Nielsen, Claus
AU - Ellegaard, Kirsten
AU - Larsen, Nicolai Balle
AU - Hartmann, Esben Mørk
AU - Jensen, Anders
AU - Sørensen, Karina Meden
AU - Østergaard, Stine K.
AU - Sørensen, Emil A.
AU - Jensen, Thomas B. N.
AU - Fuster-Collados, Emilio
AU - Chiche-Lapierre, Clarisse
AU - Andersen, Kasper S.
AU - Michaelsen, Thomas Y.
AU - Petersen, Celine
AU - Hansen, Susan H.
AU - Krarup, Henrik Bygum
AU - Schønning, Kristian
AU - Paulsen, Sarah Juel
AU - Schneider, Uffe Vest
AU - Pedersen, Martin Schou
AU - Castruita, Jose Alfredo Samaniego
AU - Thomsen, Marianne Kragh
AU - Ellermann-Eriksen, Svend
AU - Thomsen, Karina Gravgaard
AU - Andersen, Dorte Terp
AU - Steinke, Kat
AU - Skov, Marianne Nielsine
AU - Larsen, Sanne Løkkegaard
AU - Hoppe, Morten
AU - Sundelin, Thomas
AU - Coia, John E.
AU - Laugesen, Asta Lili
AU - Johansen, Rikke Lykke
AU - Nielsen, Xiaohui
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
PY - 2024/8/20
Y1 - 2024/8/20
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.
U2 - 10.1038/s41467-024-51371-0
DO - 10.1038/s41467-024-51371-0
M3 - Journal article
SN - 2041-1723
VL - 15
JO - Nature Communications
JF - Nature Communications
IS - 1
M1 - 7123
ER -