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

Abstract

. Delta's emergence in the UK occurred on the background of a heterogeneous landscape of immunity and relaxation of non-pharmaceutical interventions. Here we analyse 52,992 virus genomes from England together with 93,649 global genomes 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. Through analysis of human movement, contact tracing, and virus genomic data, we find that the geographic focus of Delta's expansion shifted from India to a more global pattern in early May 2021. In England, Delta lineages were introduced >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 transmission chains that later dominated England's Delta wave were seeded before travel restrictions were introduced. Increasing inter-regional travel within England drove Delta's nationwide dissemination, with some cities receiving >2,000 observable lineage introductions from elsewhere. Subsequently, increased levels of local population mixing, not the number of importations, were associated with faster relative growth of Delta. Delta's invasion dynamics depended on spatial heterogeneity in contact patterns, and our findings will inform optimal spatial interventions to reduce transmission of current and future variant of concern, such as Omicron.

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