Genomic reconstruction of the SARS-CoV-2 epidemic in England
Harald Vöhringer, Theo Sanderson, Matthew Sinnott, Nicola De Maio, Thuy Nguyen, Richard Goater, Frank Schwach, Ian Harrison, Joel Hellewell, Cristina V. Ariani, Sónia Gonçalves, David K. Jackson, Ian Johnston, Alexander W. Jung, Callum Saint, John Sillitoe, Maria Suciu, Nick Goldman, Jasmina Panovska‐Griffiths, Irina Abnizova, Louise Aigrain, Alex Alderton, Mozam Ali, Laura Allen, Roberto Amato, Ralph Anderson, Cristina V. Ariani, Siobhan Austin-Guest, Sendu Bala, Jeffrey C. Barrett, Andrew R. Bassett, Kristina Battleday, James R. Beal, Mathew A. Beale, Charlotte Beaver, Sam Bellany, Tristram Bellerby, Katie Bellis, Duncan Berger, Matthew Berriman, Emma Betteridge, Paul Bevan, Simon Binley, Jason Bishop, Kirsty Blackburn, James Bonfield, Nick Boughton, Sam Bowker, Timothy Brendler-Spaeth, Iraad F. Bronner, Tanya Brooklyn, Sarah K. Buddenborg, R.L. Bush, Catarina Caetano, Alex Cagan, Nicola Carter, Joanna Cartwright, Tiago Monteiro, Liz Chapman, Tracey-Jane Chillingworth, Peter Clapham, Richard Clark, Adrian Clarke, Catriona Clarke, Daryl Cole, Elizabeth Cook, Maria Coppola, Linda Cornell, Clare Cornwell, Craig Corton, Abby Crackett, Alison Cranage, Harriet Craven, Sarah Craw, Mark Crawford, Tim Cutts, Monika Dabrowska, Matt Davies, Robert M. Davies, Joseph Dawson, Callum Day, Aiden Densem, Thomas Dibling, Cat Dockree, D. C. Dodd, Sunil Kumar Dogga, Matthew J. Dorman, Gordon Dougan, Martin Dougherty, Alexander Dove, Lucy Drummond, Eleanor Drury, Monika Dudek, Jillian Durham, Laura Durrant, Elizabeth Easthope, Sabine Eckert, Peter Ellis, Ben W. Farr, Michael Fenton
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.