Genomic assessment of invasion dynamics of SARS-CoV-2 Omicron BA.1

Joseph L-H Tsui, John T McCrone, Ben Lambert, Sumali Bajaj, Rhys P D Inward, Paolo Bosetti, Rosario Evans Pena, Houriiyah Tegally, Verity Hill, Alexander E Zarebski, Thomas P Peacock, Luyang Liu, Neo Wu, Megan Davis, Isaac I Bogoch, Kamran Khan, Meaghan Kall, Nurin Iwani Binti Abdul Aziz, Rachel Colquhoun, Áine O'TooleBen Jackson, Abhishek Dasgupta, Eduan Wilkinson, Tulio de Oliveira, Thomas R Connor, Nicholas J Loman, Vittoria Colizza, Christophe Fraser, Erik Volz, Xiang Ji, Bernardo Gutierrez, Meera Chand, Simon Dellicour, Simon Cauchemez, Jayna Raghwani, Marc A Suchard, Philippe Lemey, Andrew Rambaut, Oliver G Pybus, Moritz U G Kraemer

Research output: Contribution to journalArticlepeer-review

Abstract / Description of output

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants of concern (VOCs) now arise in the context of heterogeneous human connectivity and population immunity. Through a large-scale phylodynamic analysis of 115,622 Omicron BA.1 genomes, we identified >6,000 introductions of the antigenically distinct VOC into England and analyzed their local transmission and dispersal history. We find that six of the eight largest English Omicron lineages were already transmitting when Omicron was first reported in southern Africa (22 November 2021). Multiple datasets show that importation of Omicron continued despite subsequent restrictions on travel from southern Africa as a result of export from well-connected secondary locations. Initiation and dispersal of Omicron transmission lineages in England was a two-stage process that can be explained by models of the country's human geography and hierarchical travel network. Our results enable a comparison of the processes that drive the invasion of Omicron and other VOCs across multiple spatial scales.

Original languageEnglish
Pages (from-to)336-343
Number of pages8
JournalScience (New York, N.Y.)
Issue number6655
Publication statusPublished - 21 Jul 2023

Keywords / Materials (for Non-textual outputs)

  • Humans
  • Africa, Southern
  • COVID-19/transmission
  • Genomics
  • SARS-CoV-2/classification
  • Phylogeny


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