MOOD publications

@article{doi:10.1126/science.abf2946,

title = {Establishment and lineage dynamics of the SARS-CoV-2 epidemic in the UK},

author = {Louis Plessis and John T. McCrone and Alexander E. Zarebski and Verity Hill and Christopher Ruis and Bernardo Gutierrez and Jayna Raghwani and Jordan Ashworth and Rachel Colquhoun and Thomas R. Connor and Nuno R. Faria and Ben Jackson and Nicholas J. Loman and Áine O’Toole and Samuel M. Nicholls and Kris V. Parag and Emily Scher and Tetyana I. Vasylyeva and Erik M. Volz and Alexander Watts and Isaac I. Bogoch and Kamran Khan and null and David M. Aanensen and Moritz U. G. Kraemer and Andrew Rambaut and Oliver G. Pybus},

doi = {10.1126/science.abf2946 URL = https://www.science.org/doi/abs/10.1126/science.abf2946},

year  = {2021},

date = {2021-01-01},

urldate = {2021-01-01},

journal = {Science},

volume = {371},

number = {6530},

pages = {708-712},

abstract = {The scale of genome-sequencing efforts for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is unprecedented. The United Kingdom has contributed more than 26,000 sequences to this effort. This volume of data allowed du Plessis et al. to develop a detailed picture of the influxes of virus reaching U.K. shores as the pandemic developed during the first months of 2020 (see the Perspective by Nelson). Before lockdown, high travel volumes and few restrictions on international travel allowed more than 1000 lineages to become established. This accelerated local epidemic growth and exceeded contact tracing capacity. The authors were able to quantify the abundance, size distribution, and spatial range of the lineages that were transmitted. Transmission was highly heterogeneous, favoring some lineages that became widespread and subsequently harder to eliminate. This dire history indicates that rapid or even preemptive responses should have been used as they were elsewhere where containment was successful. Science, this issue p. 708; see also p. 680 Large-scale virus genome sequencing reveals the genetic structure and importation dynamics of a national COVID-19 epidemic. 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.},

keywords = {COVID-19, epidemiology, genome, phylogenetic, travel, United Kingdom},

pubstate = {published},

tppubtype = {article}

}