ArticleScience (New York, N.Y.)2021
Establishment and lineage dynamics of the SARS-CoV-2 epidemic in the UK.
Article in Science (New York, N.Y.), 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 278 papers.
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Who cites it
278 citing papers in PubMed.
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- Global approaches to infectious disease surveillance and modeling.Nature medicine · 2026Review
- Optimizing global genomic surveillance for early detection of emerging SARS-CoV-2 variants.Nature communications · 2026Article
- Navigating the mysterious space of evolutionary histories.Proceedings of the National Academy of Sciences of the United States of America · 2026Article
- Multicountry genomic analysis underscores regional cholera spread in Africa.Nature communications · 2026Article
- Reconstructing the early spatial spread of pandemic respiratory viruses in the United States.Proceedings of the National Academy of Sciences of the United States of America · 2026Article
- Biological causes and impacts of rugged tree landscapes in phylodynamic inference.Proceedings of the National Academy of Sciences of the United States of America · 2026Article
- Widening East-West inequality in life expectancy in Europe during the COVID-19 pandemic: An international comparative study.PloS one · 2026Article
- Transmission Dynamics of Torque Teno Sus Virus 1 (TTSuV1) Between Wild and Farmed Pigs: A Molecular Tool for Monitoring Cross-Population Spillover in Swine.Microorganisms · 2025Article
- Uncovering heterogeneous intercommunity disease transmission from neutral allele frequency time series.Proceedings of the National Academy of Sciences of the United States of America · 2025Article
- ARTreeFormer: A faster attention-based autoregressive model for phylogenetic inference.PLoS computational biology · 2025Article
- Review
- Historical and current spatiotemporal patterns of wild and vaccine-derived poliovirus spread.Nature microbiology · 2025Article
- Reconstructing the early spatial spread of pandemic respiratory viruses in the United States.medRxiv : the preprint server for health sciences · 2025Article
- Phylodynamics of SARS-CoV-2 Lineages B.1.1.7, B.1.1.529 and B.1.617.2 in Nigeria Suggests Divergent Evolutionary Trajectories.Pathogens (Basel, Switzerland) · 2025Article
- Capturing the spatiotemporal spread of COVID-19 in 30 European countries during 2020 - 2022.BMC public health · 2025Article
- Predicting the trend of SARS-CoV-2 mutation frequencies using historical data.Bioinformatics (Oxford, England) · 2025Article
- HIPSTR: highest independent posterior subtree reconstruction in TreeAnnotator X.Bioinformatics (Oxford, England) · 2025Article
218 more citing papers are in PubMed but not listed here.
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27 authors.
Funding
Abstract
The United Kingdom's COVID-19 epidemic during early 2020 was one of world's largest and was unusually well represented by virus genomic sampling. We determined the fine-scale genetic lineage structure of this epidemic through analysis of 50,887 severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) genomes, including 26,181 from the UK sampled throughout the country's first wave of infection. Using large-scale phylogenetic analyses combined with epidemiological and travel data, we quantified the size, spatiotemporal origins, and persistence of genetically distinct UK transmission lineages. Rapid fluctuations in virus importation rates resulted in >1000 lineages; those introduced prior to national lockdown tended to be larger and more dispersed. Lineage importation and regional lineage diversity declined after lockdown, whereas lineage elimination was size-dependent. We discuss the implications of our genetic perspective on transmission dynamics for COVID-19 epidemiology and control.
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