Dispersal patterns and influence of air travel during the global expansion of SARS-CoV-2 variants of concern.

Humans Air Travel COVID-19 Phylogeny SARS-CoV-2
SARS-CoV-2 genomics global dispersal mobility phylogenetics phylogeography travel variants

Journal

Cell
ISSN: 1097-4172
Titre abrégé: Cell
Pays: United States
ID NLM: 0413066

Informations de publication

Date de publication:
20 07 2023
Historique:
received: 22 11 2022
revised: 31 05 2023
accepted: 02 06 2023
medline: 26 7 2023
pubmed: 7 7 2023
entrez: 6 7 2023
Statut: ppublish

Résumé

The Alpha, Beta, and Gamma SARS-CoV-2 variants of concern (VOCs) co-circulated globally during 2020 and 2021, fueling waves of infections. They were displaced by Delta during a third wave worldwide in 2021, which, in turn, was displaced by Omicron in late 2021. In this study, we use phylogenetic and phylogeographic methods to reconstruct the dispersal patterns of VOCs worldwide. We find that source-sink dynamics varied substantially by VOC and identify countries that acted as global and regional hubs of dissemination. We demonstrate the declining role of presumed origin countries of VOCs in their global dispersal, estimating that India contributed <15% of Delta exports and South Africa <1%-2% of Omicron dispersal. We estimate that >80 countries had received introductions of Omicron within 100 days of its emergence, associated with accelerated passenger air travel and higher transmissibility. Our study highlights the rapid dispersal of highly transmissible variants, with implications for genomic surveillance along the hierarchical airline network.

Identifiants

DOI: 10.1016/j.cell.2023.06.001 PMID: 37413988 PMC: PMC10247138
pubmed: 37413988
pii: S0092-8674(23)00641-4
doi: 10.1016/j.cell.2023.06.001
pmc: PMC10247138
pii:
doi:

Types de publication

Journal Article Research Support, N.I.H., Extramural Research Support, Non-U.S. Gov't

Langues

eng

Sous-ensembles de citation

IM

Pagination

3277-3290.e16

Subventions

Organisme : Wellcome Trust
ID : 222574/Z/21/Z
Pays : United Kingdom
Organisme : Wellcome Trust
ID : 225288/Z/22/Z
Pays : United Kingdom
Organisme : Wellcome Trust
ID : 204311/Z/16/Z
Pays : United Kingdom
Organisme : Medical Research Council
ID : MR/S0195/1
Pays : United Kingdom

Commentaires et corrections

Type : UpdateOf

Informations de copyright

Copyright © 2023 The Authors. Published by Elsevier Inc. All rights reserved.

Déclaration de conflit d'intérêts

Declaration of interests K.K. is the founder of BlueDot, a social enterprise that develops digital technologies for public health. C.H. is employed at BlueDot.

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Auteurs

Houriiyah Tegally (H)

Centre for Epidemic Response and Innovation (CERI), School of Data Science and Computational Thinking, Stellenbosch University, Stellenbosch, South Africa; KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), Nelson R. Mandela School of Medicine, University of KwaZulu-Natal, Durban, South Africa. Electronic address: houriiyah.tegally@gmail.com.

Eduan Wilkinson (E)

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

Joseph L-H Tsui (JL)

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

Monika Moir (M)

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

Darren Martin (D)

Wellcome Centre for Infectious Diseases Research in Africa (CIDRI-Africa), Cape Town, South Africa; Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Cape Town, South Africa.

Anderson Fernandes Brito (AF)

Instituto Todos pela Saúde, São Paulo, São Paulo, Brazil.

Marta Giovanetti (M)

Laboratorio de Flavivirus, Fundacao Oswaldo Cruz, Rio de Janeiro, Brazil; Laboratório de Genética Celular e Molecular, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil; Department of Science and Technology for Humans and the Environment, University of Campus Bio-Medico di Roma, Rome, Italy.

Kamran Khan (K)

BlueDot, Toronto, ON, Canada; Department of Medicine, Division of Infectious Diseases, University of Toronto, Toronto, ON, Canada.

Carmen Huber (C)

BlueDot, Toronto, ON, Canada.

Isaac I Bogoch (II)

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

James Emmanuel San (JE)

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

Jenicca Poongavanan (J)

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

Joicymara S Xavier (JS)

Centre for Epidemic Response and Innovation (CERI), School of Data Science and Computational Thinking, Stellenbosch University, Stellenbosch, South Africa; Universidade Federal de Minas Gerais, Belo Horizonte, Brazil; Institute of Agricultural Sciences, Universidade Federal dos Vales do Jequitinhonha e Mucuri, Unaí, Brazil.

Darlan da S Candido (DDS)

MRC Centre for Global Infectious Disease Analysis and Department of Infectious Disease Epidemiology, Jameel Institute, School of Public Health, Imperial College London, London, UK.

Filipe Romero (F)

MRC Centre for Global Infectious Disease Analysis and Department of Infectious Disease Epidemiology, Jameel Institute, School of Public Health, Imperial College London, London, UK.

Cheryl Baxter (C)

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

Oliver G Pybus (OG)

Department of Biology, University of Oxford, Oxford, UK; Pandemic Sciences Institute, University of Oxford, Oxford, UK; Department of Pathobiology and Population Sciences, Royal Veterinary College London, London, UK.

Richard J Lessells (RJ)

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

Nuno R Faria (NR)

Department of Biology, University of Oxford, Oxford, UK; MRC Centre for Global Infectious Disease Analysis and Department of Infectious Disease Epidemiology, Jameel Institute, School of Public Health, Imperial College London, London, UK; Departamento de Moléstias Infecciosas e Parasitárias e Instituto de Medicina Tropical da Faculdade de Medicina, Universidade de São Paulo, São Paulo, Brazil.

Moritz U G Kraemer (MUG)

Department of Biology, University of Oxford, Oxford, UK; Pandemic Sciences Institute, University of Oxford, Oxford, UK. Electronic address: moritz.kraemer@biology.ox.ac.uk.

Tulio de Oliveira (T)

Centre for Epidemic Response and Innovation (CERI), School of Data Science and Computational Thinking, Stellenbosch University, Stellenbosch, South Africa; KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), Nelson R. Mandela School of Medicine, University of KwaZulu-Natal, Durban, South Africa; Department of Global Health, University of Washington, Seattle, WA, USA. Electronic address: tulio@sun.ac.za.

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Classifications MeSH

questionsmedicales.fr › Eucaryotes › Animaux › Chordés › Vertébrés › Mammifères › Eutheria › Primates › Haplorhini › Catarrhini › Hominidae › Humains › Dispersal patterns and influence of air travel...
questionsmedicales.fr › Activités humaines › Voyage › Voyage aérien › Dispersal patterns and influence of air travel...
questionsmedicales.fr › Maladies de l'appareil respiratoire › Infections de l'appareil respiratoire › Pneumopathie infectieuse › Pneumopathie virale › COVID-19 › Dispersal patterns and influence of air travel...
questionsmedicales.fr › Sciences de l'information › Phylogenèse › Dispersal patterns and influence of air travel...
questionsmedicales.fr › Virus › Virus à ARN › Virus à ARN à brin positif › Nidovirales › Coronaviridae › Coronavirus › Betacoronavirus › Virus du SRAS › SARS-CoV-2 › Dispersal patterns and influence of air travel...