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'Toole; Ben 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

doi:10.1126/science.adg6605

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'Toole

Ben 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^*

^*Corresponding author for this work

University of Oxford
EaStCHEM School of Chemistry, University of Edinburgh
Helix OpCo LLC
University of Exeter
Université Paris Cité
University of KwaZulu-Natal
Stellenbosch University
Yale University
Imperial College London
UK Health Security Agency
Alphabet Inc.
BlueDot Inc.
University of Toronto Faculty of Medicine
Public Health Wales
Cardiff University
Quadram Institute
University of Birmingham
Universite Pierre et Marie Curie
Nuffield Department of Medicine
Tulane University School of Science and Engineering
Universidad San Francisco de Quito
Université Libre de Bruxelles
KU Leuven
Royal Veterinary College University of London
University of California at Los Angeles

Research output: Contribution to journal › Article › peer-review

45 Scopus citations

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.

Original language	English
Pages (from-to)	336-343
Number of pages	8
Journal	Science
Volume	381
Issue number	6655
DOIs	https://doi.org/10.1126/science.adg6605
State	Published - 21 Jul 2023
Externally published	Yes

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Tsui, J. L. H., McCrone, J. T., Lambert, B., Bajaj, S., Inward, R. P. D., Bosetti, P., Pena, R. E., Tegally, H., Hill, V., Zarebski, A. E., Peacock, T. P., Liu, L., Wu, N., Davis, M., Bogoch, I. I., Khan, K., Kall, M., Aziz, N. I. B. A., Colquhoun, R., ... Kraemer, M. U. G. (2023). Genomic assessment of invasion dynamics of SARS-CoV-2 Omicron BA.1. Science, 381(6655), 336-343. https://doi.org/10.1126/science.adg6605

@article{aac88398e3ef4f649349c95f8ad8e86a,

title = "Genomic assessment of invasion dynamics of SARS-CoV-2 Omicron BA.1",

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.",

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

year = "2023",

month = jul,

day = "21",

doi = "10.1126/science.adg6605",

language = "Ingl{\'e}s",

volume = "381",

pages = "336--343",

journal = "Science",

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publisher = "American Association for the Advancement of Science",

number = "6655",

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Tsui, JLH, McCrone, JT, Lambert, B, Bajaj, S, Inward, RPD, Bosetti, P, Pena, RE, Tegally, H, Hill, V, Zarebski, AE, Peacock, TP, Liu, L, Wu, N, Davis, M, Bogoch, II, Khan, K, Kall, M, Aziz, NIBA, Colquhoun, R, O'Toole, Á, Jackson, B, Dasgupta, A, Wilkinson, E, de Oliveira, T, Connor, TR, Loman, NJ, Colizza, V, Fraser, C, Volz, E, Ji, X, Gutierrez, B, Chand, M, Dellicour, S, Cauchemez, S, Raghwani, J, Suchard, MA, Lemey, P, Rambaut, A, Pybus, OG & Kraemer, MUG 2023, 'Genomic assessment of invasion dynamics of SARS-CoV-2 Omicron BA.1', Science, vol. 381, no. 6655, pp. 336-343. https://doi.org/10.1126/science.adg6605

TY - JOUR

T1 - Genomic assessment of invasion dynamics of SARS-CoV-2 Omicron BA.1

AU - Tsui, Joseph L.H.

AU - McCrone, John T.

AU - Lambert, Ben

AU - Bajaj, Sumali

AU - Inward, Rhys P.D.

AU - Bosetti, Paolo

AU - Pena, Rosario Evans

AU - Tegally, Houriiyah

AU - Hill, Verity

AU - Zarebski, Alexander E.

AU - Peacock, Thomas P.

AU - Liu, Luyang

AU - Wu, Neo

AU - Davis, Megan

AU - Bogoch, Isaac I.

AU - Khan, Kamran

AU - Kall, Meaghan

AU - Aziz, Nurin Iwani Binti Abdul

AU - Colquhoun, Rachel

AU - O'Toole, Áine

AU - Jackson, Ben

AU - Dasgupta, Abhishek

AU - Wilkinson, Eduan

AU - de Oliveira, Tulio

AU - Connor, Thomas R.

AU - Loman, Nicholas J.

AU - Colizza, Vittoria

AU - Fraser, Christophe

AU - Volz, Erik

AU - Ji, Xiang

AU - Gutierrez, Bernardo

AU - Chand, Meera

AU - Dellicour, Simon

AU - Cauchemez, Simon

AU - Raghwani, Jayna

AU - Suchard, Marc A.

AU - Lemey, Philippe

AU - Rambaut, Andrew

AU - Pybus, Oliver G.

AU - Kraemer, Moritz U.G.

PY - 2023/7/21

Y1 - 2023/7/21

N2 - 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.

AB - 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.

UR - https://www.scopus.com/pages/publications/85165423791

U2 - 10.1126/science.adg6605

DO - 10.1126/science.adg6605

M3 - Artículo

C2 - 37471538

AN - SCOPUS:85165423791

SN - 0036-8075

VL - 381

SP - 336

EP - 343

JO - Science

JF - Science

IS - 6655

ER -

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

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