Instruct: Identify the main category of Medrxiv papers based on the titles and abstracts
Query: Context-specific emergence and growth of the SARS-CoV-2 Delta variant The Delta variant of concern of SARS-CoV-2 has spread globally causing large outbreaks and resurgences of COVID-19 cases1-3. The emergence of Delta in the UK occurred on the background of a heterogeneous landscape of immunity and relaxation of non-pharmaceutical interventions4,5. Here we analyse 52,992 Delta genomes from England in combination 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 focus of geographic expansion of Delta 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 from India reduced onward transmission from importations; however the transmission chains that later dominated the Delta wave in England had been already seeded before restrictions were introduced. In England, increasing inter-regional travel drove Deltas nationwide dissemination, with some cities receiving >2,000 observable lineage introductions from other regions. Subsequently, increased levels of local population mixing, not the number of importations, was associated with faster relative growth of Delta. Among US states, we find that regions that previously experienced large waves also had faster Delta growth rates, and a model including interactions between immunity and human behaviour could accurately predict the rise of Delta there. Deltas invasion dynamics depended on fine scale spatial heterogeneity in immunity and contact patterns and our findings will inform optimal spatial interventions to reduce transmission of current and future VOCs such as Omicron.
43
The categories of this paper are: environmental
1
The categories of this paper are: sports
32
The categories of this paper are: rehabilitation
27
The categories of this paper are: quality
25
The categories of this paper are: improvement
69
The categories of this paper are: palliative
13
The categories of this paper are: genetic
51
The categories of this paper are: education
65
The categories of this paper are: oral
17
The categories of this paper are: informatics
3
The categories of this paper are: sexual
73
The categories of this paper are: toxicology
63
The categories of this paper are: pain
60
The categories of this paper are: addiction
20
The categories of this paper are: psychiatry
18
The categories of this paper are: global