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In addition to measuring genetic diversity, understanding pathogen lineage dynamics can help researchers to target interventions effectively, track variants with potentially different phenotypes, and improve the interpretation of incidence data. Such studies show that regional epidemics can be highly dynamic at the genetic level, with recurrent importation and extinction of transmission chains within a given location. However, recent studies of Ebola, Zika, influenza, and other viruses have demonstrated that virus emergence and spread can instead be tracked using large-scale pathogen genome sequencing. Although individual-level contact-tracing investigations can reconstruct the structure of small-scale transmission clusters, they cannot be extended practically to large national epidemics. Infectious disease epidemics are composed of chains of transmission, yet surprisingly little is known about how co-circulating transmission lineages vary in size, spatial distribution, and persistence, or how key properties such as epidemic size and duration arise from their combined action. We discuss the implications of our genetic perspective on transmission dynamics for COVID-19 epidemiology and control. Lineage importation and regional lineage diversity declined after lockdown, whereas lineage elimination was size-dependent. Rapid fluctuations in virus importation rates resulted in >1000 lineages those introduced prior to national lockdown tended to be larger and more dispersed. 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. 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. 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. This dire history indicates that rapid or even preemptive responses should have been used as they were elsewhere where containment was successful.
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Transmission was highly heterogeneous, favoring some lineages that became widespread and subsequently harder to eliminate. The authors were able to quantify the abundance, size distribution, and spatial range of the lineages that were transmitted. This accelerated local epidemic growth and exceeded contact tracing capacity. Before lockdown, high travel volumes and few restrictions on international travel allowed more than 1000 lineages to become established. shores as the pandemic developed during the first months of 2020 (see the Perspective by Nelson). to develop a detailed picture of the influxes of virus reaching U.K. This volume of data allowed du Plessis et al.
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The United Kingdom has contributed more than 26,000 sequences to this effort. The scale of genome-sequencing efforts for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is unprecedented. Bogoch, Kamran Khan, COVID-19 Genomics UK (COG-UK) Consortium †, David M. Zarebski, Verity Hill, Christopher Ruis, Bernardo Gutierrez, Jayna Raghwani, … Show All …, Jordan Ashworth, Rachel Colquhoun, Thomas R.