SARS-CoV-2 within-host diversity and transmission.
Eyre, David W
Oxford Virus Sequencing Analysis Group (OVSG),
COVID-19 Genomics UK (COG-UK) Consortium,
Science (New York, N.Y.)
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Lythgoe, K. A., Hall, M., Ferretti, L., de Cesare, M., MacIntyre-Cockett, G., Trebes, A., Andersson, M., et al. (2021). SARS-CoV-2 within-host diversity and transmission.. Science (New York, N.Y.), 372 (6539)https://doi.org/10.1126/science.abg0821
Extensive global sampling and sequencing of the pandemic virus 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 characterise within-host diversity and transmission we deep-sequenced 1313 clinical samples from the UK. SARS-CoV-2 infections are characterised by low levels of within-host diversity when viral loads are high, and 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 which are readily observable on the phylogenetic tree. Our results suggest that transmission-enhancing and/or immune-escape variants are likely to arise infrequently, but could spread rapidly if successfully transmitted.
Oxford Virus Sequencing Analysis Group (OVSG), COVID-19 Genomics UK (COG-UK) Consortium, Humans, Coronavirus OC43, Human, Coronavirus Infections, RNA, Viral, Viral Load, Family Characteristics, Phylogeny, Mutation, Genome, Viral, Genetic Variation, Selection, Genetic, Immune Evasion, Coinfection, Spike Glycoprotein, Coronavirus, United Kingdom, RNA-Seq, COVID-19, SARS-CoV-2
We gratefully acknowledge the UK COVID-19 Genomics Consortium (COG UK) for funding. COG-UK is supported by funding from the Medical Research Council (MRC) part of UK Research & Innovation (UKRI), the National Institute of Health Research (NIHR), and Genome Research Limited, operating as the Wellcome Sanger Institute.
External DOI: https://doi.org/10.1126/science.abg0821
This record's URL: https://www.repository.cam.ac.uk/handle/1810/318640
Attribution 4.0 International
Licence URL: https://creativecommons.org/licenses/by/4.0/