@article{Vhringer_H-2021_59308,
title = {Genomic reconstruction of the SARS-CoV-2 epidemic in England},
author = {Vöhringer, H. and Sanderson, T. and Sinnott, M. and De Maio, N. and Nguyen, T. and Goater, R. and Schwach, F. and Harrison, I. and Hellewell, J. and Ariani, C. and Gonçalves, S. and Jackson, D. and Johnston, I. and Jung, A. and Saint, C. and Sillitoe, J. and Suciu, M. and Goldman, N. and Panovska-Griffiths, J. and Birney, E. and Volz, E. and Funk, S. and Kwiatkowski, D. and Chand, M. and Martincorena, I. and Barrett, J. and Gerstung, M. and Abnizova, I. and Aigrain, L. and Alderton, A. and Ali, M. and Allen, L. and Amato, R. and Anderson, R. and Ariani, C. and Austin-Guest, S. and Bala, S. and Barrett, J. and Bassett, A. and Battleday, K. and Beal, J. and Beale, M. and Beaver, C. and Bellany, S. and Bellerby, T. and Bellis, K. and Berger, D. and Berriman, M. and Betteridge, E. and Bevan, P. and Binley, S. and Bishop, J. and Blackburn, K. and Bonfield, J. and Boughton, N. and Bowker, S. and Brendler-Spaeth, T. and Bronner, I. and Brooklyn, T. and Buddenborg, S. and Bush, R. and Caetano, C. and Cagan, A. and Carter, N. and Cartwright, J. and Monteiro, T. and Chapman, L. and Chillingworth, T. and Clapham, P. and Clark, R. and Clarke, A. and Clarke, C. and Cole, D. and Cook, E. and Coppola, M. and Cornell, L. and Cornwell, C. and Corton, C. and Crackett, A. and Cranage, A. and Craven, H. and Craw, S. and Crawford, M. and Cutts, T. and Dabrowska, M. and Davies, M. and Davies, R. and Dawson, J. and Day, C. and Densem, A. and Dibling, T. and Dockree, C. and Dodd, D. and Dogga, S. and Dorman, M. and Dougan, G. and Dougherty, M. and Dove, A. and Drummond, L. and Drury, E. and Dudek, M. and Durham, J. and Durrant, L. and Easthope, E. and Eckert, S. and Ellis, P. and Farr, B. and Fenton, M. and Ferrero, M. and Flack, N. and Fordham, H. and Forsythe, G. and Foulser, L. and Francis, M. and Fraser, A. and Freeman, A. and Galvin, A. and Garcia-Casado, M. and Gedny, A. and Girgis, S. and Glover, J. and Gonçalves, S. and Goodwin, S. and Gould, O. and Gourtovaia, M. and Gray, A. and Gray, E. and Griffiths, C. and Gu, Y. and Guerin, F. and Hamilton, W. and Hanks, H. and Harrison, E. and Harrott, A. and Harry, E. and Harvison, J. and Heath, P. and Hernandez-Koutoucheva, A. and Hobbs, R. and Holland, D. and Holmes, S. and Hornett, G. and Hough, N. and Huckle, L. and Hughes-Hallet, L. and Hunter, A. and Inglis, S. and Iqbal, S. and Jackson, A. and Jackson, D. and James, K. and Jamrozy, D. and Verdejo, C. and Jones, M. and Kallepally, K. and Kane, L. and Kay, K. and Kay, S. and Keatley, J. and Keith, A. and King, A. and Kitchin, L. and Kleanthous, M. and Klimekova, M. and Korlevic, P. and Krasheninnkova, K. and Lane, G. and Langford, C. and Laverack, A. and Law, K. and Lawniczak, M. and Lensing, S. and Leonard, S. and Letchford, L. and Lewis, K. and Lewis-Wade, A. and Liddle, J. and Lin, Q. and Lindsay, S. and Linsdell, S. and Livett, R. and Lo, S. and Long, R. and Lovell, J. and Lovell, J. and Ludden, C. and Mack, J. and Maddison, M. and Makunin, A. and 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Rudder, S. and Baxter, C. and Carvalho, S. and Lavin, D. and Mariappan, A. and Radulescu, C. and Singh, A. and Tang, M. and Morcrette, H. and Bayzid, N. and Cotic, M. and Balcazar, C. and Gallagher, M. and Maloney, D. and Stanton, T. and Williamson, K. and Manley, R. and Michelsen, M. and Sambles, C. and Studholme, D. and Warwick-Dugdale, J. and Eccles, R. and Gemmell, M. and Gregory, R. and Hughes, M. and Nelson, C. and Rainbow, L. and Vamos, E. and Webster, H. and Whitehead, M. and Wierzbicki, C. and Angyal, A. and Green, L. and Whiteley, M. and Bronner, I. and Farr, B. and Lensing, S. and McCarthy, S. and Quail, M. and Redshaw, N. and Thurston, S. and Rowe, W. and Gaskin, A. and Le-Viet, T. and Liddle, J.},
month = {dec},
year = {2021},
abstract = {The evolution of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) virus leads to new variants that warrant timely epidemiological characterization. Here we use the dense genomic surveillance data generated by the COVID-19 Genomics UK Consortium to reconstruct the dynamics of 71 different lineages in each of 315 English local authorities between September 2020 and June 2021. This analysis reveals a series of subepidemics that peaked in early autumn 2020, followed by a jump in transmissibility of the B.1.1.7/Alpha lineage. The Alpha variant grew when other lineages declined during the second national lockdown and regionally tiered restrictions between November and December 2020. A third more stringent national lockdown suppressed the Alpha variant and eliminated nearly all other lineages in early 2021. Yet a series of variants (most of which contained the spike E484K mutation) defied these trends and persisted at moderately increasing proportions. However, by accounting for sustained introductions, we found that the transmissibility of these variants is unlikely to have exceeded the transmissibility of the Alpha variant. Finally, B.1.617.2/Delta was repeatedly introduced in England and grew rapidly in early summer 2021, constituting approximately 98% of sampled SARS-CoV-2 genomes on 26 June 2021.},
volume = {600},
journal = {Nature},
publisher = {Springer Nature},
url = {https://doi.org/10.1038/s41586-021-04069-y},
}
