2024 PQG Conference

Verity Hill

Verity Hill, MSc
PhD student
University of Ediburgh

 

The origins, evolution and spread of B.1.1.7 in the UK

The SARS-CoV-2 lineage B.1.1.7 (also known as Alpha) likely arose in Kent, in South East England. It is defined phylogenetically by an exceptionally long branch, with 23 lineage-defining mutations. We use phylodynamic techniques to explore the rate of evolution across the tree in order to examine possible explanations for the origins for B.1.1.7. The rate of evolution on this branch is higher than in the background lineages, and within B.1.1.7 itself. This combined with the high sampling proportion in the UK and the lack of sampled secondary transmission chains suggests that this lineage evolved within a single, chronically infected patient.

We also undertook an analysis combining human movement data with densely sampled viral genomic data, and a continuous phylogeographic analysis to explore how B.1.1.7 spread within England. We found that movement from London and Kent was highly predictive of date for first arrival in an Upper Tier Local Authority (UTLA) area in England, further supporting the idea that B.1.1.7 truly did spread across the country from the South East of England. We were also able to explore source-sink dynamics, and examine the role of non-pharmaceutical interventions in the spread of B.1.1.7.

Verity Hill*1, Simon Dellicour2,3, Chris Ruis4, Oliver Pybus5, Moritz Kraemer5 ,Andrew Rambaut1

  1. Institute of Evolutionary Biology, University of Edinburgh, Edinburgh, UK
  2. Spatial Epidemiology Lab (SpELL), Université Libre de Bruxelles, Bruxelles, Belgium
  3. Department of Microbiology, Immunology and Transplantation, Rega Institute, KU Leuven, 3000 Leuven, Belgium
  1. Molecular Immunity Unit, Department of Medicine, Cambridge University, Cambridge, UK
  1. Department of Zoology, University of Oxford, Oxford, UK