Establishment and lineage dynamics of the SARS-CoV-2 epidemic in the UK

Author(s):Show less -

du Plessis, Louis ^[1] ; McCrone, John T. ^[2] ; Zarebski, Alexander E. ^[1] ; Hill, Verity ^[2] ; Ruis, Christopher ^{[3, 4]} ; Gutierrez, Bernardo ^{[1, 5]} ; Raghwani, Jayna ^[1] ; Ashworth, Jordan ^[2] ; Colquhoun, Rachel ^[2] ; Connor, Thomas R. ^{[6, 7]} ; Faria, Nuno R. ^{[1, 8]} ; Jackson, Ben ^[2] ; Loman, Nicholas J. ^[9] ; O'Toole, Aine ^[2] ; Nicholls, Samuel M. ^[9] ; Parag, V, Kris ; Scher, Emily ^[2] ; Vasylyeva, I, Tetyana ; Volz, Erik M. ^[10] ; Watts, Alexander ^{[11, 12]} ; Bogoch, Isaac I. ^{[13, 14]} ; Khan, Kamran ^{[13, 11, 12]} ; Aanensen, David M. ^{[15, 16]} ; Kraemer, Moritz U. G. ^[17] ; Rambaut, Andrew ^[2] ; Pybus, Oliver G. ^{[17, 18]} ; Consor, COVID-19 Gcnomics UK COG-UK

Affiliation:Show less -

^[1] Univ Oxford, Dept Zool, Oxford - England

^[2] Univ Edinburgh, Inst Evolutionary Biol, Edinburgh, Midlothian - Scotland

^[3] Univ Cambridge, Dept Vet Med, Cambridge - England

^[4] Univ Cambridge, Dept Med, Mol Immun Unit, Cambridge - England

^[5] Univ San Francisco Quito, Sch Biol & Environm Sci, Quito - Ecuador

^[6] Cardiff Univ, Sch Biosci, Cardiff - Wales

^[7] Publ Hlth Wales NHS Trust, Pathogen Genom Unit, Cardiff - Wales

^[8] Imperial Coll London, MRC Ctr Global Infect Dis Anal, J IDEA, London - England

^[9] Univ Birmingham, Inst Microbiol & Infect, Birmingham, W Midlands - England

^[10] Parag, Kris, V, Imperial Coll London, MRC Ctr Global Infect Dis Anal, J IDEA, London - England

^[11] St Michaels Hosp, Li Ka Shing Knowledge Inst, Toronto, ON - Canada

^[12] BlueDot, Toronto, ON - Canada

^[13] Univ Toronto, Dept Med, Toronto, ON - Canada

^[14] Univ Hlth Network, Div Gen Internal Med, Toronto, ON - Canada

^[15] Ctr Genom Pathogen Surveillance, Wellcome Genome Campus, Hinxton - England

^[16] Univ Oxford, Li Ka Shing Ctr Hlth Informat & Discovery, Big Data Inst, Nuffield Dept Med, Oxford - England

^[17] Vasylyeva, Tetyana, I, Univ Oxford, Dept Zool, Oxford - England

^[18] Royal Vet Coll London, Dept Pathobiol & Populat Sci, London - England

• Document type: Journal article
• Source: Science; v. 371, n. 6530, p. 708+, FEB 12 2021.
• Web of Science Citations: 9

Abstract

The United Kingdom's COVID-19 epidemic during early 2020 was one of world's largest and was unusually well represented by virus genomic sampling. We determined the fine-scale genetic lineage structure of this epidemic through analysis of 50,887 severe acute respiratory syndrome coronavirus 2 (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 quantified the size, spatiotemporal origins, and persistence of genetically distinct UK transmission lineages. Rapid fluctuations in virus importation rates resulted in >1000 lineages; those introduced prior to national lockdown tended to be larger and more dispersed. Lineage importation and regional lineage diversity declined after lockdown, whereas lineage elimination was size-dependent. We discuss the implications of our genetic perspective on transmission dynamics for COVID-19 epidemiology and control. (AU)

• FAPESP's process: 18/14389-0 - Brazil-UK Centre for Arbovirus Discovery, Diagnosis, Genomics and Epidemiology (CADDE)
• Grantee: Ester Cerdeira Sabino
• Support Opportunities: Research Projects - Thematic Grants