SARS-CoV-2 within-host diversity and transmission

Oxford Virus Sequencing Analysis Group (OVSG), COVID-19 Genomics UK (COG-UK) Consortium

Research output: Contribution to journalArticlepeer-review

9 Citations (Scopus)


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.

Original languageEnglish
Article numbereabg0821
Issue number6539
Publication statusPublished - 16 Apr 2021
Externally publishedYes

Bibliographical note

Funding Information:
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. The research was also supported by a Wellcome Core Award (203141/Z/16/Z) with additional funding from the NIHR Oxford Biomedical Research Centre. The views expressed are those of the authors and not necessarily those of the NHS, the NIHR, or the Department of Health. K.A.L. and M.A.A. were supported by The Wellcome Trust and The Royal Society (107652/Z/15/Z to K.A.L. and 220171/Z/20/Z to M.A.A.). M.H., L.F., M.d.C., G.M.C., N.O., L.A.D., D.B., C.F., and T.G. were supported by Li Ka Shing Foundation funding awarded to C.F. P.S. was supported by a Wellcome Investigator Award (WT103767MA). J.A.T. was supported by a Wellcome Core Award (203141/Z/16/Z). C.E.M. was supported by the Fleming Fund at the Department of Health and Social Care, UK; the Wellcome Trust (209142/Z/17/Z) and the Bill and Melinda Gates Foundation (OPP1176062). DWE is a Robertson Fellow and an NIHR Oxford BRC Senior Fellow.

Publisher Copyright:
© 2021 American Association for the Advancement of Science. All rights reserved.


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