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

Authors: McCrone, John T; Hill, Verity; Bajaj, Sumali; Pena, Rosario Evans; Lambert, Ben C; Inward, Rhys; Bhatt, Samir; +34 Authors

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

Abstract

AbstractThe SARS-CoV-2 Delta (Pango lineage B.1.617.2) variant of concern spread globally, causing resurgences of COVID-19 worldwide1,2. 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

DYNAMICS, General Science & Technology, 610, Genome, Viral, Article, COVID-19 Genomics UK (COG-UK) Consortium, Humans, Viral, Cities, 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, Travel, Genome, Science & Technology, SARS-CoV-2, COVID-19, Généralités, 004, Multidisciplinary Sciences, Emerging Infectious Diseases, Infectious Diseases, Good Health and Well Being, England, Quarantine, Science & Technology - Other Topics, Contact Tracing

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    selected citations
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    This is an alternative to the "Influence" indicator, which also reflects the overall/total impact of an article in the research community at large, based on the underlying citation network (diachronically).
    104
    popularity
    This indicator reflects the "current" impact/attention (the "hype") of an article in the research community at large, based on the underlying citation network.
    Top 1%
    influence
    This indicator reflects the overall/total impact of an article in the research community at large, based on the underlying citation network (diachronically).
    Top 10%
    impulse
    This indicator reflects the initial momentum of an article directly after its publication, based on the underlying citation network.
    Top 1%
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selected citations
These citations are derived from selected sources.
This is an alternative to the "Influence" indicator, which also reflects the overall/total impact of an article in the research community at large, based on the underlying citation network (diachronically).
BIP!Citations provided by BIP!
popularity
This indicator reflects the "current" impact/attention (the "hype") of an article in the research community at large, based on the underlying citation network.
BIP!Popularity provided by BIP!
influence
This indicator reflects the overall/total impact of an article in the research community at large, based on the underlying citation network (diachronically).
BIP!Influence provided by BIP!
impulse
This indicator reflects the initial momentum of an article directly after its publication, based on the underlying citation network.
BIP!Impulse provided by BIP!
104
Top 1%
Top 10%
Top 1%
Green
hybrid