Genomic assessment of invasion dynamics of SARS-CoV-2 Omicron BA.1
成果类型：
Article
署名作者：
Tsui, Joseph L. -H.; McCrone, John T.; Lambert, Ben; Bajaj, Sumali; Inward, Rhys P. D.; Bosetti, Paolo; Pena, Rosario Evans; Tegally, Houriiyah; Hill, Verity; Zarebski, Alexander E.; Peacock, Thomas P.; Liu, Luyang; Wu, Neo; Davis, Megan; Bogoch, Isaac I.; Khan, Kamran; Kall, Meaghan; Aziz, Nurin Iwani Binti Abdul; Colquhoun, Rachel; O'Toole, Aine; Jackson, Ben; Dasgupta, Abhishek; Wilkinson, Eduan; de Oliveira, Tulio; Connor, Thomas R.; Loman, Nicholas J.; Colizza, Vittoria; Fraser, Christophe; Volz, Erik; Ji, Xiang; Gutierrez, Bernardo; Chand, Meera; Dellicour, Simon; Cauchemez, Simon; Raghwani, Jayna; Suchard, Marc A.; Lemey, Philippe; Rambaut, Andrew; Pybus, Oliver G.; Kraemer, Moritz U. G.
署名单位：
University of Oxford; University of Edinburgh; University of Exeter; Centre National de la Recherche Scientifique (CNRS); Pasteur Network; Universite Paris Cite; Institut Pasteur Paris; University of Kwazulu Natal; Stellenbosch University; Yale University; Imperial College London; UK Health Security Agency (UKHSA); Alphabet Inc.; Google Incorporated; University of Toronto; University of Oxford; Cardiff University; UK Research & Innovation (UKRI); Biotechnology and Biological Sciences Research Council (BBSRC); Quadram Institute; University of Birmingham; Institut National de la Sante et de la Recherche Medicale (Inserm); Sorbonne Universite; University of Oxford; University of Oxford; Imperial College London; Tulane University; Universidad San Francisco de Quito; Universite Libre de Bruxelles; KU Leuven; University of London; University of London Royal Veterinary College; University of California System; University of California Los Angeles
刊物名称：
SCIENCE
ISSN/ISSBN：
0036-11890
DOI：
10.1126/science.adg6605
发表日期：
2023-07-21
页码：
336-343
关键词：
摘要：
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants of concern (VOCs) now arise in the context of heterogeneous human connectivity and population immunity. Through a large-scale phylodynamic analysis of 115,622 Omicron BA.1 genomes, we identified >6,000 introductions of the antigenically distinct VOC into England and analyzed their local transmission and dispersal history. We find that six of the eight largest English Omicron lineages were already transmitting when Omicron was first reported in southern Africa (22 November 2021). Multiple datasets show that importation of Omicron continued despite subsequent restrictions on travel from southern Africa as a result of export from well-connected secondary locations. Initiation and dispersal of Omicron transmission lineages in England was a two-stage process that can be explained by models of the country's human geography and hierarchical travel network. Our results enable a comparison of the processes that drive the invasion of Omicron and other VOCs across multiple spatial scales.