Dataset Information

Establishment and lineage dynamics of the SARS-CoV-2 epidemic in the UK.

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.

SUBMITTER: du Plessis L

PROVIDER: S-EPMC7877493 | biostudies-literature | 2021 Feb

REPOSITORIES: biostudies-literature

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Establishment and lineage dynamics of the SARS-CoV-2 epidemic in the UK.

du Plessis Louis L McCrone John T JT Zarebski Alexander E AE Hill Verity V Ruis Christopher C Gutierrez Bernardo B Raghwani Jayna J Ashworth Jordan J Colquhoun Rachel R Connor Thomas R TR Faria Nuno R NR Jackson Ben B Loman Nicholas J NJ O'Toole Áine Á Nicholls Samuel M SM Parag Kris V KV Scher Emily E Vasylyeva Tetyana I TI Volz Erik M EM Watts Alexander A Bogoch Isaac I II Khan Kamran K Aanensen David M DM Kraemer Moritz U G MUG Rambaut Andrew A Pybus Oliver G OG

Science (New York, N.Y.) 20210108 6530

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 quantifi ...[more]

PMID: 33419936

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Project description:The first SARS-CoV-2 variant of concern (VOC) to be designated was lineage B.1.1.7, later labelled by the World Health Organization as Alpha. Originating in early autumn but discovered in December 2020, it spread rapidly and caused large waves of infections worldwide. The Alpha variant is notable for being defined by a long ancestral phylogenetic branch with an increased evolutionary rate, along which only two sequences have been sampled. Alpha genomes comprise a well-supported monophyletic clade within which the evolutionary rate is typical of SARS-CoV-2. The Alpha epidemic continued to grow despite the continued restrictions on social mixing across the UK and the imposition of new restrictions, in particular, the English national lockdown in November 2020. While these interventions succeeded in reducing the absolute number of cases, the impact of these non-pharmaceutical interventions was predominantly to drive the decline of the SARS-CoV-2 lineages that preceded Alpha. We investigate the only two sampled sequences that fall on the branch ancestral to Alpha. We find that one is likely to be a true intermediate sequence, providing information about the order of mutational events that led to Alpha. We explore alternate hypotheses that can explain how Alpha acquired a large number of mutations yet remained largely unobserved in a region of high genomic surveillance: an under-sampled geographical location, a non-human animal population, or a chronically infected individual. We conclude that the latter provides the best explanation of the observed behaviour and dynamics of the variant, although the individual need not be immunocompromised, as persistently infected immunocompetent hosts also display a higher within-host rate of evolution. Finally, we compare the ancestral branches and mutation profiles of other VOCs and find that Delta appears to be an outlier both in terms of the genomic locations of its defining mutations and a lack of the rapid evolutionary rate on its ancestral branch. As new variants, such as Omicron, continue to evolve (potentially through similar mechanisms), it remains important to investigate the origins of other variants to identify ways to potentially disrupt their evolution and emergence.

Dataset Information

Establishment and lineage dynamics of the SARS-CoV-2 epidemic in the UK.

Publications

Establishment and lineage dynamics of the SARS-CoV-2 epidemic in the UK.

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