ArticleScience (New York, N.Y.)2021
SARS-CoV-2 within-host diversity and transmission.
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Article in Science (New York, N.Y.), 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 276 papers.
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276citing papers in PubMed
24.4field-weighted citation impact, top 1% of its field
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Who cites it
276 citing papers in PubMed, 426 citations in OpenAlex.
- Transmission of mutated SARS-CoV-2 variants is favored by relatively prolonged infections due to delayed immunity.bioRxiv : the preprint server for biology · 2026Article
- SARS-CoV-2 intra-host variation shows evidence of transmission and convergent evolution in a university surveillance cohort.Microbial genomics · 2026Article
- Identification and masking of artifactual and misleading within-host variants in deep-sequencing SARS-CoV-2 data.Molecular biology and evolution · 2026Article
- Detecting and supporting COVID-19 outbreak response in a small-scale nursing home through passive wastewater surveillance of SARS-CoV-2.Applied and environmental microbiology · 2026Article
- Dose-dependent effects of recombinant spike protein-based vaccination on SARS-CoV-2 evolutionary dynamics and the emergence of variants in hamster models.The Journal of general virology · 2026Article
- Within-host SARS-CoV-2 diversity in immunocompromised patients during acute infection.Journal of virology · 2026Article
- Comparing frequentist and Bayesian methods to identify drivers of pathogen strain invasion: A temporal case study of pertussis in the United States.Infectious Disease Modelling · 2026Article
- Strain-level transmission inference across multi-kingdom metagenomic data using TRACS.Nature microbiology · 2026Article
- SARS-CoV-2 intra-host viral diversity associated with host innate and vaccine-induced immunity in an obese mouse model.BMC infectious diseases · 2026Article
- Kinship Analysis Confirms Tolerant Galapagos Mockingbirds Are a Source of Nest Flies That Threaten Darwin's Finches.Molecular ecology · 2026Article
- Extensive evolution and T cell escape by SARS-CoV-2 in a 2.5-year persistent infection of an immunocompromised host.iScience · 2026Article
- VICAST: An Integrated Toolkit for Viral Genome Annotation Curation and Low-Frequency Variant Analysis in Passage Studies.bioRxiv : the preprint server for biology · 2026Article
- Antibody escape drives emergence of diverse spike haplotypes resembling variants of concern in persistent SARS-CoV-2 infections.Cell reports. Medicine · 2026Article
- Respiratory virus genomic epidemiology during post-pandemic re-emergence of influenza in Australia.Virus evolution · 2026Article
- Shared quasispecies architecture in experimental and natural RNA virus populations.Virus evolution · 2026Article
- Near Neutral Selectionist Theories (NNST) for SARS-CoV-2 suggested by the substitution-mutation ratio (c/µ) analysis.PloS one · 2026Article
- SARS-CoV-2 intra-host evolution during acute infection in COVID-19 patients.Frontiers in microbiology · 2026Article
- Genomic evolution and minority variant dynamics of RSV during the first season of nirsevimab implementation in Italy (2024-5).Virus evolution · 2026Article
- SARS-CoV-2 Intra-host Variation Shows Evidence of Transmission and Convergent Evolution in a University Surveillance Cohort.bioRxiv : the preprint server for biology · 2025Article
- SARS-CoV-2 within-host population expansion, diversification and adaptation in zoo tigers, lions and hyenas.Nature communications · 2025Article
216 more citing papers are in PubMed but not listed here.
Corrections and comments
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Authors and funding
38 authors at 10 institutions in 3 countries.
Katrina A Lythgoe *Big Data Institute, Nuffield Department of Medicine, University of Oxford, Old Road Campus, Oxford OX3 7LF, UK. Tanya.Golubchik@bdi.ox.ac.uk Katrina.Lythgoe@bdi.ox.ac.uk Matthew.Hall@bdi.ox.ac.uk.ORCID https://orcid.org/0000-0002-7089-7680
Matthew Hall *Big Data Institute, Nuffield Department of Medicine, University of Oxford, Old Road Campus, Oxford OX3 7LF, UK. Tanya.Golubchik@bdi.ox.ac.uk Katrina.Lythgoe@bdi.ox.ac.uk Matthew.Hall@bdi.ox.ac.uk.ORCID https://orcid.org/0000-0002-2671-3864
Luca FerrettiBig Data Institute, Nuffield Department of Medicine, University of Oxford, Old Road Campus, Oxford OX3 7LF, UK.ORCID https://orcid.org/0000-0001-7578-7301
Mariateresa de CesareBig Data Institute, Nuffield Department of Medicine, University of Oxford, Old Road Campus, Oxford OX3 7LF, UK.ORCID https://orcid.org/0000-0002-9847-1526
George MacIntyre-CockettBig Data Institute, Nuffield Department of Medicine, University of Oxford, Old Road Campus, Oxford OX3 7LF, UK.
Amy TrebesWellcome Centre for Human Genetics, Nuffield Department of Medicine, NIHR Biomedical Research Centre, University of Oxford, Old Road Campus, Oxford OX3 7BN, UK.ORCID https://orcid.org/0000-0002-3715-9109
Monique AnderssonOxford University Hospitals NHS Foundation Trust, John Radcliffe Hospital, Headington, Oxford OX3 9DU, UK.ORCID https://orcid.org/0000-0003-0619-1074
Newton OteckoBig Data Institute, Nuffield Department of Medicine, University of Oxford, Old Road Campus, Oxford OX3 7LF, UK.
Emma L WiseHampshire Hospitals NHS Foundation Trust, Basingstoke and North Hampshire Hospital, Basingstoke RG24 9NA, UK.ORCID https://orcid.org/0000-0002-0279-3900
Nathan MooreHampshire Hospitals NHS Foundation Trust, Basingstoke and North Hampshire Hospital, Basingstoke RG24 9NA, UK.ORCID https://orcid.org/0000-0002-4279-2443
Jessica LynchHampshire Hospitals NHS Foundation Trust, Basingstoke and North Hampshire Hospital, Basingstoke RG24 9NA, UK.ORCID https://orcid.org/0000-0003-2015-9986
Stephen KiddHampshire Hospitals NHS Foundation Trust, Basingstoke and North Hampshire Hospital, Basingstoke RG24 9NA, UK.ORCID https://orcid.org/0000-0002-4504-4600
Nicholas CortesHampshire Hospitals NHS Foundation Trust, Basingstoke and North Hampshire Hospital, Basingstoke RG24 9NA, UK.
Matilde MoriSchool of Medicine, University of Southampton, Southampton SO17 1BJ, UK.ORCID https://orcid.org/0000-0001-9012-1911
Rebecca WilliamsHampshire Hospitals NHS Foundation Trust, Basingstoke and North Hampshire Hospital, Basingstoke RG24 9NA, UK.ORCID https://orcid.org/0000-0002-8557-6337
Gabrielle VernetHampshire Hospitals NHS Foundation Trust, Basingstoke and North Hampshire Hospital, Basingstoke RG24 9NA, UK.ORCID https://orcid.org/0000-0001-9887-2824
Anita JusticeOxford University Hospitals NHS Foundation Trust, John Radcliffe Hospital, Headington, Oxford OX3 9DU, UK.
Angie GreenWellcome Centre for Human Genetics, Nuffield Department of Medicine, NIHR Biomedical Research Centre, University of Oxford, Old Road Campus, Oxford OX3 7BN, UK.ORCID https://orcid.org/0000-0003-4386-9972
Samuel M NichollsInstitute of Microbiology and Infection, University of Birmingham, Birmingham B15 2TT, UK.ORCID https://orcid.org/0000-0003-4081-065X
M Azim AnsariPeter Medawar Building for Pathogen Research, University of Oxford, Oxford OX1 3SY, UK.ORCID https://orcid.org/0000-0003-2790-8353
Lucie Abeler-DörnerBig Data Institute, Nuffield Department of Medicine, University of Oxford, Old Road Campus, Oxford OX3 7LF, UK.ORCID https://orcid.org/0000-0003-3662-4192
Catrin E MooreBig Data Institute, Nuffield Department of Medicine, University of Oxford, Old Road Campus, Oxford OX3 7LF, UK.ORCID https://orcid.org/0000-0002-8639-9846
Timothy E A PetoOxford University Hospitals NHS Foundation Trust, John Radcliffe Hospital, Headington, Oxford OX3 9DU, UK.ORCID https://orcid.org/0000-0003-3477-8307
David W EyreOxford University Hospitals NHS Foundation Trust, John Radcliffe Hospital, Headington, Oxford OX3 9DU, UK.
Robert ShawOxford University Hospitals NHS Foundation Trust, John Radcliffe Hospital, Headington, Oxford OX3 9DU, UK.ORCID https://orcid.org/0000-0003-3449-5876
Peter SimmondsPeter Medawar Building for Pathogen Research, University of Oxford, Oxford OX1 3SY, UK.
David BuckWellcome Centre for Human Genetics, Nuffield Department of Medicine, NIHR Biomedical Research Centre, University of Oxford, Old Road Campus, Oxford OX3 7BN, UK.
John A ToddWellcome Centre for Human Genetics, Nuffield Department of Medicine, NIHR Biomedical Research Centre, University of Oxford, Old Road Campus, Oxford OX3 7BN, UK.ORCID https://orcid.org/0000-0003-2740-8148
Oxford Virus Sequencing Analysis Group (OVSG)
Thomas R ConnorPathogen Genomics Unit, Public Health Wales Microbiology, Cardiff CF10 4BZ, UK.ORCID https://orcid.org/0000-0003-2394-6504
Shirin AshrafMRC-University of Glasgow Centre for Virus Research, Glasgow G61 1QH, UK.ORCID https://orcid.org/0000-0002-6468-0258
Ana da Silva FilipeMRC-University of Glasgow Centre for Virus Research, Glasgow G61 1QH, UK.ORCID https://orcid.org/0000-0002-9442-2903
James ShepherdMRC-University of Glasgow Centre for Virus Research, Glasgow G61 1QH, UK.ORCID https://orcid.org/0000-0003-3915-048X
Emma C ThomsonMRC-University of Glasgow Centre for Virus Research, Glasgow G61 1QH, UK.ORCID https://orcid.org/0000-0003-1482-0889
COVID-19 Genomics UK (COG-UK) Consortium
David BonsallBig Data Institute, Nuffield Department of Medicine, University of Oxford, Old Road Campus, Oxford OX3 7LF, UK.ORCID https://orcid.org/0000-0003-2187-0550
Christophe FraserBig Data Institute, Nuffield Department of Medicine, University of Oxford, Old Road Campus, Oxford OX3 7LF, UK.ORCID https://orcid.org/0000-0003-2399-9657
Tanya GolubchikBig Data Institute, Nuffield Department of Medicine, University of Oxford, Old Road Campus, Oxford OX3 7LF, UK. Tanya.Golubchik@bdi.ox.ac.uk Katrina.Lythgoe@bdi.ox.ac.uk Matthew.Hall@bdi.ox.ac.uk.ORCID https://orcid.org/0000-0003-2765-9828
Centre for Human Genetics · GBUniversity of Oxford · GBHampshire Hospitals NHS Foundation Trust · GBJohn Radcliffe Hospital · GBMRC University of Glasgow Centre for Virus Research · GBPublic Health Wales · GBStellenbosch University · ZAUniversity of Birmingham · GBUniversity of Southampton · GBUniversity of Surrey · GB
Funding
Medical Research Council MC_PC_19027
Abstract
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.
Indexed as
Genetic VariationCoinfectionCoronavirus InfectionsCoronavirus OC43, HumanCOVID-19Family CharacteristicsGenome, ViralHumansImmune EvasionMutationPhylogenyRNA-SeqRNA, ViralSARS-CoV-2Selection, GeneticSpike Glycoprotein, CoronavirusRNA, ViralSpike Glycoprotein, Coronavirusspike protein, SARS-CoV-2
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Read underepoch 390
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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.