TY - JOUR
AU - McCrone, John T.
AU - Hill, Verity
AU - Bajaj, Sumali
AU - Pena, Rosario Evans
AU - Lambert, Ben C.
AU - Inward, Rhys
AU - Bhatt, Samir
AU - Volz, Erik
AU - Ruis, Christopher
AU - Dellicour, Simon
AU - Baele, Guy
AU - Zarebski, Alexander E.
AU - Sadilek, Adam
AU - Wu, Neo
AU - Schneider, Aaron
AU - Ji, Xiang
AU - Raghwani, Jayna
AU - Jackson, Ben
AU - Colquhoun, Rachel M.
AU - O'Toole, Áine Niamh
AU - Peacock, Thomas P.
AU - Twohig, Kate
AU - Thelwall, Simon
AU - Dabrera, Gavin
AU - Myers, Richard
AU - COVID-19 Genomics UK (COG-UK) consortium
AU - Faria, Nuno Rodrigues
AU - Huber, Carmen
AU - Bogoch, Isaac I.
AU - Khan, Kamran
AU - du Plessis, Louis
AU - Barrett, Jeffrey C.
AU - Aanensen, David M.
AU - Barclay, Wendy S.
AU - Chand, Meera
AU - Connor, Thomas R.
AU - Loman, Nicholas J.
AU - Suchard, Marc A.
AU - Pybus, Oliver G.
AU - Rambaut, Andrew
AU - Kraemer, Moritz U.G.
PY - 2021
DA - December
TI - Context specific emergence and growth of the SARS-CoV-2 Delta variant [Preprint]
JO - MedRxiv
DO - https://doi.org/10.1101/2021.12.14.21267606
AB - The Delta variant of concern of SARS-CoV-2 has spread globally causing large outbreaks and resurgences of COVID-19 cases. The emergence of Delta in the UK occurred on the background of a heterogeneous landscape of immunity and relaxation of non-pharmaceutical interventions. 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 &gt;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 Delta’s nationwide dissemination, with some cities receiving &gt;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. Delta’s 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.
PB - medRxiv
UR - https://publichealthscotland.scot/id/80684
KW - Coronavirus (COVID-19)
ER