Journal
SCIENCE
Volume 372, Issue 6539, Pages 256-+Publisher
AMER ASSOC ADVANCEMENT SCIENCE
DOI: 10.1126/science.abg0821
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Funding
- UK COVID-19 Genomics Consortium (COG UK)
- Medical Research Council (MRC) part of UK Research & Innovation (UKRI)
- National Institute of Health Research (NIHR)
- Genome Research Limited
- Wellcome Core Award [203141/Z/16/Z]
- NIHR Oxford Biomedical Research Centre
- Wellcome Trust [209142/Z/17/Z]
- Royal Society [107652/Z/15/Z, 220171/Z/20/Z]
- Li Ka Shing Foundation
- Wellcome Investigator Award [WT103767MA]
- Fleming Fund at the Department of Health and Social Care, UK
- Bill and Melinda Gates Foundation [OPP1176062]
- Wellcome Trust
- Bill and Melinda Gates Foundation [OPP1176062] Funding Source: Bill and Melinda Gates Foundation
- Wellcome Trust [107652/Z/15/Z] Funding Source: Wellcome Trust
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The study found that SARS-CoV-2 infections in clinical samples in the UK are characterized by low levels of within-host diversity and a narrow bottleneck at transmission. Most variants are either lost or occasionally fixed at the point of transmission, with shared diversity not persisting.
Extensive global sampling and sequencing of the pandemic virus severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) have enabled researchers to monitor its spread and to identify concerning new variants. Two important determinants of variant spread are how frequently they arise within individuals and how likely they are to be transmitted. To characterize within-host diversity and transmission, we deep-sequenced 1313 clinical samples from the United Kingdom. SARS-CoV-2 infections are characterized by low levels of within-host diversity when viral loads are high and by a narrow bottleneck at transmission. Most variants are either lost or occasionally fixed at the point of transmission, with minimal persistence of shared diversity, patterns that are readily observable on the phylogenetic tree. Our results suggest that transmission-enhancing and/or immune-escape SARS-CoV-2 variants are likely to arise infrequently but could spread rapidly if successfully transmitted.
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