Genomic assessment of invasion dynamics of SARS-CoV-2 Omicron BA.1-Reference-Cited by-同舟云学术

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

Published:2023-07-21 Issue:6655 Volume:381 Page:336-343
ISSN:0036-8075
Container-title:Science
language:en
Short-container-title:Science

Author:

Tsui Joseph L.-H.¹^ORCID,McCrone John T.²³^ORCID,Lambert Ben⁴^ORCID,Bajaj Sumali¹^ORCID,Inward Rhys P. D.¹^ORCID,Bosetti Paolo⁵^ORCID,Pena Rosario Evans¹,Tegally Houriiyah⁶⁷^ORCID,Hill Verity²⁸,Zarebski Alexander E.¹^ORCID,Peacock Thomas P.⁹¹⁰^ORCID,Liu Luyang¹¹,Wu Neo¹¹^ORCID,Davis Megan¹²^ORCID,Bogoch Isaac I.¹³^ORCID,Khan Kamran¹²¹³^ORCID,Kall Meaghan¹⁰^ORCID,Abdul Aziz Nurin Iwani Binti¹⁰^ORCID,Colquhoun Rachel²^ORCID,O’Toole Áine²^ORCID,Jackson Ben²^ORCID,Dasgupta Abhishek¹¹⁴^ORCID,Wilkinson Eduan⁶⁷^ORCID,de Oliveira Tulio⁶⁷^ORCID,Connor Thomas R.¹⁵¹⁶¹⁷^ORCID,Loman Nicholas J.¹⁸^ORCID,Colizza Vittoria¹⁹^ORCID,Fraser Christophe²⁰²¹^ORCID,Volz Erik²²^ORCID,Ji Xiang²³^ORCID,Gutierrez Bernardo¹²⁴^ORCID,Chand Meera¹⁰,Dellicour Simon²⁵²⁶^ORCID,Cauchemez Simon⁵^ORCID,Raghwani Jayna¹²⁷^ORCID,Suchard Marc A.²⁸^ORCID,Lemey Philippe²⁶^ORCID,Rambaut Andrew²^ORCID,Pybus Oliver G.¹²¹²⁷^ORCID,Kraemer Moritz U. G.¹²¹^ORCID,

Affiliation:

1. Department of Biology, University of Oxford, Oxford, UK.

2. Institute of Ecology and Evolution, University of Edinburgh, Edinburgh, UK.

3. Helix, San Mateo, CA 94401, USA.

4. College of Engineering, Mathematics and Physical Sciences, University of Exeter, Exeter, UK.

5. Institut Pasteur, Université Paris Cité, CNRS, Paris, France.

6. KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), Nelson R. Mandela School of Medicine, University of KwaZulu-Natal, Durban, South Africa.

7. Centre for Epidemic Response and Innovation (CERI), School for Data Science and Computational Thinking, Stellenbosch University, Stellenbosch, South Africa.

8. Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT 06511, USA.

9. Department of Infectious Disease, Imperial College London, London, UK.

10. UK Health Security Agency, London, UK.

11. Google Research, Mountain View, CA 94043, USA.

12. BlueDot, Toronto, Canada.

13. Department of Medicine, Division of Infectious Diseases, University of Toronto, Toronto, Canada.

14. Doctoral Training Centre, University of Oxford, Oxford, UK.

15. Pathogen Genomics Unit, Public Health Wales NHS Trust, Cardiff, UK.

16. School of Biosciences, The Sir Martin Evans Building, Cardiff University, Cardiff, UK.

17. Quadram Institute, Norwich, UK.

18. Institute of Microbiology and Infection, University of Birmingham, Birmingham, UK.

19. Sorbonne Université, INSERM, Institut Pierre Louis d’Épidémiologie et de Santé Publique (IPLESP), Paris, France.

20. Big Data Institute, Li Ka Shing Centre for Health Information and Discovery, Nuffield Department of Medicine, University of Oxford, UK.

21. Pandemic Sciences Institute, University of Oxford, Oxford, UK.

22. MRC Centre of Global Infectious Disease Analysis, Jameel Institute for Disease and Emergency Analytics, Imperial College London, London, UK.

23. Department of Mathematics, Tulane University, New Orleans, LA 70118, USA.

24. School of Biological and Environmental Sciences, Universidad San Francisco de Quito USFQ, Quito, Ecuador.

25. Spatial Epidemiology Lab (SpELL), Université Libre de Bruxelles, Bruxelles, Belgium.

26. Department of Microbiology, Immunology and Transplantation, Rega Institute, KU Leuven, Leuven, Belgium.

27. Department of Pathobiology and Population Science, Royal Veterinary College, London, UK.

28. Departments of Biostatistics, Biomathematics and Human Genetics, University of California, Los Angeles, CA 90095, USA.

Abstract

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.

Publisher

American Association for the Advancement of Science (AAAS)

Subject

Multidisciplinary

Reference82 articles.

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