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

Louis Du Plessis ,David M Aanensen ,Jayna Raghwani ,Chris Ruis ,John Mccrone ,Tetyana I Vasylyeva ,Jordan Ashworth ,Alexander E Zarebski ,Moritz U G Kraemer ,Isaac I Bogoch ,Thomas R Connor ,Emily Scher ,Kamran Khan ,Andrew Rambaut ,Verity Hill ,Áine O’toole ,Samuel M Nicholls ,Nicholas J Loman ,Erik Volz ,Bernardo Gutierrez ,Nuno Rodrigues Faria ,Rachel Colquhoun ,Alexander Watts ,Kris V Parag ,Benjamin C Jackson ,Oliver G Pybus

doi:10.1126/science.abf2946

Abstract

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 >1000 lineages; those introduced prior to national lockdown tended to be larger and more dispersed. Lineage importation and regional lineage diversity declined after lockdown, while lineage elimination was size-dependent. We discuss the implications of our genetic perspective on transmission dynamics for COVID-19 epidemiology and control.

Highlights

Using large-scale phylogenetic analyses combined with epidemiological and travel data, we quantified the size, Genetic structure and lineage dynamics of the UK epidemic from January to June spatiotemporal origins, and persistence of genetically distinct UK transmission lineages
The exceptional size of our genomic survey provides insight into the micro-epidemiological patterns that underlie the features of a large, national COVID-19 epidemic, allowing us to quantify the abundance, size distribution, and spatial range of transmission lineages
We expect that similar trends occurred in other countries with comparably large epidemics and high international travel volumes; virus genomic studies from regions with smaller or controlled COVID-19 epidemics have reported high importation rates followed by more transient lineage persistence [e.g., [28,29,30]]

Summary

Introduction

Using large-scale phylogenetic analyses combined with epidemiological and travel data, we quantified the size, Genetic structure and lineage dynamics of the UK epidemic from January to June spatiotemporal origins, and persistence of genetically distinct UK transmission lineages. Most transmission lineages are small, and 72.4% (95% HPD, 69.3 to 72.9%) contain

Results

Conclusion