Context-specific emergence and growth of the SARS-CoV-2 Delta variant.

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Version: Final published version
License: CC BY 4.0
Serval ID
serval:BIB_828438A9A01B
Type
Article: article from journal or magazin.
Collection
Publications
Institution
Title
Context-specific emergence and growth of the SARS-CoV-2 Delta variant.
Journal
Nature
Author(s)
McCrone J.T., Hill V., Bajaj S., Pena R.E., Lambert B.C., Inward R., Bhatt S., Volz E., Ruis C., Dellicour S., Baele G., Zarebski A.E., Sadilek A., Wu N., Schneider A., Ji X., Raghwani J., Jackson B., Colquhoun R., O'Toole Á., Peacock T.P., Twohig K., Thelwall S., Dabrera G., Myers R., Faria N.R., Huber C., Bogoch I.I., Khan K., du Plessis L., Barrett J.C., Aanensen D.M., Barclay W.S., Chand M., Connor T., Loman N.J., Suchard M.A., Pybus O.G., Rambaut A., Kraemer MUG
Working group(s)
COVID-19 Genomics UK (COG-UK) Consortium
ISSN
1476-4687 (Electronic)
ISSN-L
0028-0836
Publication state
Published
Issued date
10/2022
Peer-reviewed
Oui
Volume
610
Number
7930
Pages
154-160
Language
english
Notes
Publication types: Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't
Publication Status: ppublish
Abstract
The SARS-CoV-2 Delta (Pango lineage B.1.617.2) variant of concern spread globally, causing resurgences of COVID-19 worldwide <sup>1,2</sup> . The emergence of the Delta variant in the UK occurred on the background of a heterogeneous landscape of immunity and relaxation of non-pharmaceutical interventions. Here we analyse 52,992 SARS-CoV-2 genomes from England together with 93,649 genomes from the rest of the world to reconstruct the emergence of Delta and quantify its introduction to and regional dissemination across England in the context of changing travel and social restrictions. Using analysis of human movement, contact tracing and virus genomic data, we find that the geographic focus of the expansion of Delta shifted from India to a more global pattern in early May 2021. In England, Delta lineages were introduced more than 1,000 times and spread nationally as non-pharmaceutical interventions were relaxed. We find that hotel quarantine for travellers reduced onward transmission from importations; however, the transmission chains that later dominated the Delta wave in England were seeded before travel restrictions were introduced. Increasing inter-regional travel within England drove the nationwide dissemination of Delta, with some cities receiving more than 2,000 observable lineage introductions from elsewhere. Subsequently, increased levels of local population mixing-and not the number of importations-were associated with the faster relative spread of Delta. The invasion dynamics of Delta depended on spatial heterogeneity in contact patterns, and our findings will inform optimal spatial interventions to reduce the transmission of current and future variants of concern, such as Omicron (Pango lineage B.1.1.529).
Keywords
COVID-19/epidemiology, COVID-19/prevention & control, COVID-19/transmission, COVID-19/virology, Cities/epidemiology, Contact Tracing, England/epidemiology, Genome, Viral/genetics, Humans, Quarantine/legislation & jurisprudence, SARS-CoV-2/genetics, SARS-CoV-2/growth & development, SARS-CoV-2/isolation & purification, Travel/legislation & jurisprudence
Pubmed
Web of science
Open Access
Yes
Create date
19/10/2022 15:23
Last modification date
23/01/2024 8:29
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