TY - JOUR
AU - du Plessis, Louis
AU - McCrone, John T.
AU - Zarebski, Alexander E.
AU - Hill, Verity
AU - Ruis, Christopher
AU - Gutierrez, Bernardo
AU - Raghwani, Jayna
AU - Ashworth, Jordan
AU - Colquhoun, Rachel M.
AU - Connor, Thomas R.
AU - Faria, Nuno Rodrigues
AU - Jackson, Ben
AU - Loman, Nicholas J.
AU - O'Toole, Áine Niamh
AU - Nicholls, Samuel M.
AU - Parag, Kris V.
AU - Scher, Emily
AU - Vasylyeva, Tetyana I.
AU - Volz, Erik M.
AU - Watts, Alexander
AU - Bogoch, Isaac I.
AU - Khan, Kamran
AU - Aanensen, David M.
AU - Kraemer, Moritz U.G.
AU - Rambaut, Andrew
AU - Pybus, Oliver G.
PY - 2021
DA - February
TI - Establishment & lineage dynamics of the SARS-CoV-2 epidemic in the UK
JO - Science
EP - 712
VL - 371
IS - 6530
DO - http://dx.doi.org/10.1126/science.abf2946
AB - The UK’s COVID-19 epidemic during early 2020 was one of world’s largest and unusually well represented by virus genomic sampling. Here we reveal the fine-scale genetic lineage structure of this epidemic through analysis of 50,887 SARS-CoV-2 genomes, including 26,181 from the UK sampled throughout the country’s first wave of infection. Using large-scale phylogenetic analyses, combined with epidemiological and travel data, we quantify the size, spatio-temporal origins and persistence of genetically-distinct UK transmission lineages. Rapid fluctuations in virus importation rates resulted in &gt;1000 lineages; those introduced prior to national lockdown tended to be larger and more dispersed. Lineage importation and regional lineage diversity declined after lockdown, whilst lineage elimination was size-dependent. We discuss the implications of our genetic perspective on transmission dynamics for COVID-19 epidemiology and control.
PB - American Association for the Advancement of Science
UR - https://www.research.ed.ac.uk/portal/en/publications/establishment--lineage-dynamics-of-the-sarscov2-epidemic-in-the-uk(6bf30a28-52b0-4e0d-af5b-d3412d668ea0).html
KW - Coronavirus (COVID-19)
ER