The University of Southampton
×
Filter your search:
University of Southampton Institutional Repository

SARS-CoV-2 within-host diversity and transmission

SARS-CoV-2 within-host diversity and transmission
SARS-CoV-2 within-host diversity and transmission

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.

COVID-19/immunology, Coinfection/virology, Coronavirus Infections/virology, Coronavirus OC43, Human, Family Characteristics, Genetic Variation, Genome, Viral, Humans, Immune Evasion, Mutation, Phylogeny, RNA, Viral/genetics, RNA-Seq, SARS-CoV-2/genetics, Selection, Genetic, Spike Glycoprotein, Coronavirus/genetics, United Kingdom, Viral Load
0036-8075
Lythgoe, Katrina A.
9fdfb6f2-6d47-4f0b-98e1-043615fb89b6
Hall, Matthew
0e89d538-9e18-41b9-99ac-72399715bb6e
Ferretti, Luca
54e395ea-5fdf-4739-8ea3-93e0d033e2e5
de Cesare, Mariateresa
38ce722d-8143-4e2c-9060-09f9d7c62a56
MacIntyre-Cockett, George
ef5cec7d-e5f2-4a0d-ae24-5a1d7677c15e
Trebes, Amy
04fd3206-d8de-4b0d-9fa0-6a5e3247f549
Andersson, Monique
fe21b761-8405-4167-9838-28e5e699b8c3
Otecko, Newton
3c00bee7-aa76-48b2-87e9-606bbc8b7730
Wise, Emma L.
34bef037-e557-4b83-b971-c688bcb72bd7
Moore, Nathan
685fa518-20ce-4c8b-8cbb-bfb929a30da7
Lynch, Jessica
814a50ff-5fdb-49af-986d-b61b23324b3c
Kidd, Stephen
1409c55c-35d2-4a0b-8ef2-2370e6bf1dee
Cortes, Nicholas
72b7c08e-d1bf-40f9-823f-29bb907aeec8
Mori, Matilde
18cda4a0-217e-4911-95b6-71f8a7a7dc32
Williams, Rebecca
c8d08cdd-67bb-4322-acf4-055a81de875c
Vernet, Gabrielle
015cbc5a-ff6d-48cf-b352-1b520bd505f8
Justice, Anita
f71e0665-c9fb-4d27-9cb7-ca9a72358e24
Green, Angie
2aa54786-021c-4665-8fb1-5a31910e92b6
Nicholls, Samuel M.
24c36632-713e-4169-a136-be81509f844c
Ansari, M. Azim
6bc3f987-64de-4be7-81c4-bedf1ecb7059
Abeler-Dörner, Lucie
2b80875f-9d97-4463-ac0d-9e0e8590b51f
Moore, Catrin E.
042f3198-5a20-4507-a460-af04fae14241
Peto, Timothy E.A.
eb80abae-e536-4799-ad6a-bba3412fa2f9
Eyre, David W.
46004b8b-ece8-4250-838c-28cd18e4c132
Shaw, Robert
98582e4e-600f-40a1-bd57-c1522cf524d6
Simmonds, Peter
a2843767-f443-460c-b40c-ba1457c9196a
Buck, David
753a2f37-5031-4cc7-9f00-8065d65d782e
Todd, John A.
39de8d47-b54b-4710-8343-7d9890675970
Connor, Thomas R.
0f6acaa2-fd86-4ab0-bd67-c93d071f428c
Ashraf, Shirin
59fd4def-4e5e-4714-8fd8-4dc80326cdcd
da Silva Filipe, Ana
19807056-f55a-460b-bdec-ae306e7091e8
Shepherd, James
6d549347-4322-439b-8438-32ce08927ced
Thomson, Emma C.
c02a878f-f60f-4017-821c-962e98c01a8b
Bonsall, David
d9757249-4624-4e64-bba8-dd2308bc2e41
Fraser, Christophe
fe2f3853-4f53-4005-b92c-cdba940215b0
Golubchik, Tanya
49b63464-056c-4ecd-95a3-49f0536ff9cd
Oxford Virus Sequencing Analysis Group (OVSG)
COVID-19 Genomics UK (COG-UK) consortium
Lythgoe, Katrina A.
9fdfb6f2-6d47-4f0b-98e1-043615fb89b6
Hall, Matthew
0e89d538-9e18-41b9-99ac-72399715bb6e
Ferretti, Luca
54e395ea-5fdf-4739-8ea3-93e0d033e2e5
de Cesare, Mariateresa
38ce722d-8143-4e2c-9060-09f9d7c62a56
MacIntyre-Cockett, George
ef5cec7d-e5f2-4a0d-ae24-5a1d7677c15e
Trebes, Amy
04fd3206-d8de-4b0d-9fa0-6a5e3247f549
Andersson, Monique
fe21b761-8405-4167-9838-28e5e699b8c3
Otecko, Newton
3c00bee7-aa76-48b2-87e9-606bbc8b7730
Wise, Emma L.
34bef037-e557-4b83-b971-c688bcb72bd7
Moore, Nathan
685fa518-20ce-4c8b-8cbb-bfb929a30da7
Lynch, Jessica
814a50ff-5fdb-49af-986d-b61b23324b3c
Kidd, Stephen
1409c55c-35d2-4a0b-8ef2-2370e6bf1dee
Cortes, Nicholas
72b7c08e-d1bf-40f9-823f-29bb907aeec8
Mori, Matilde
18cda4a0-217e-4911-95b6-71f8a7a7dc32
Williams, Rebecca
c8d08cdd-67bb-4322-acf4-055a81de875c
Vernet, Gabrielle
015cbc5a-ff6d-48cf-b352-1b520bd505f8
Justice, Anita
f71e0665-c9fb-4d27-9cb7-ca9a72358e24
Green, Angie
2aa54786-021c-4665-8fb1-5a31910e92b6
Nicholls, Samuel M.
24c36632-713e-4169-a136-be81509f844c
Ansari, M. Azim
6bc3f987-64de-4be7-81c4-bedf1ecb7059
Abeler-Dörner, Lucie
2b80875f-9d97-4463-ac0d-9e0e8590b51f
Moore, Catrin E.
042f3198-5a20-4507-a460-af04fae14241
Peto, Timothy E.A.
eb80abae-e536-4799-ad6a-bba3412fa2f9
Eyre, David W.
46004b8b-ece8-4250-838c-28cd18e4c132
Shaw, Robert
98582e4e-600f-40a1-bd57-c1522cf524d6
Simmonds, Peter
a2843767-f443-460c-b40c-ba1457c9196a
Buck, David
753a2f37-5031-4cc7-9f00-8065d65d782e
Todd, John A.
39de8d47-b54b-4710-8343-7d9890675970
Connor, Thomas R.
0f6acaa2-fd86-4ab0-bd67-c93d071f428c
Ashraf, Shirin
59fd4def-4e5e-4714-8fd8-4dc80326cdcd
da Silva Filipe, Ana
19807056-f55a-460b-bdec-ae306e7091e8
Shepherd, James
6d549347-4322-439b-8438-32ce08927ced
Thomson, Emma C.
c02a878f-f60f-4017-821c-962e98c01a8b
Bonsall, David
d9757249-4624-4e64-bba8-dd2308bc2e41
Fraser, Christophe
fe2f3853-4f53-4005-b92c-cdba940215b0
Golubchik, Tanya
49b63464-056c-4ecd-95a3-49f0536ff9cd

Oxford Virus Sequencing Analysis Group (OVSG) and COVID-19 Genomics UK (COG-UK) consortium (2021) SARS-CoV-2 within-host diversity and transmission. Science, 372 (6539), [eabg0821]. (doi:10.1126/SCIENCE.ABG0821).

Record type: Article

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.

Text
science.abg0821 - Version of Record
Available under License Creative Commons Attribution.
Download (1MB)

More information

Accepted/In Press date: 3 March 2021
e-pub ahead of print date: 16 April 2021
Published date: 16 April 2021
Keywords: COVID-19/immunology, Coinfection/virology, Coronavirus Infections/virology, Coronavirus OC43, Human, Family Characteristics, Genetic Variation, Genome, Viral, Humans, Immune Evasion, Mutation, Phylogeny, RNA, Viral/genetics, RNA-Seq, SARS-CoV-2/genetics, Selection, Genetic, Spike Glycoprotein, Coronavirus/genetics, United Kingdom, Viral Load

Identifiers

Local EPrints ID: 451845
URI: http://eprints.soton.ac.uk/id/eprint/451845
DOI: doi:10.1126/SCIENCE.ABG0821
ISSN: 0036-8075
PURE UUID: 5980ad24-dacb-4caa-9c71-93d4af8fd32d

Catalogue record

Date deposited: 01 Nov 2021 17:31
Last modified: 17 Mar 2024 12:52

Export record

Altmetrics

Contributors

Author: Katrina A. Lythgoe
Author: Matthew Hall
Author: Luca Ferretti
Author: Mariateresa de Cesare
Author: George MacIntyre-Cockett
Author: Amy Trebes
Author: Monique Andersson
Author: Newton Otecko
Author: Emma L. Wise
Author: Nathan Moore
Author: Jessica Lynch
Author: Stephen Kidd
Author: Nicholas Cortes
Author: Matilde Mori
Author: Rebecca Williams
Author: Gabrielle Vernet
Author: Anita Justice
Author: Angie Green
Author: Samuel M. Nicholls
Author: M. Azim Ansari
Author: Lucie Abeler-Dörner
Author: Catrin E. Moore
Author: Timothy E.A. Peto
Author: David W. Eyre
Author: Robert Shaw
Author: Peter Simmonds
Author: David Buck
Author: John A. Todd
Author: Thomas R. Connor
Author: Shirin Ashraf
Author: Ana da Silva Filipe
Author: James Shepherd
Author: Emma C. Thomson
Author: David Bonsall
Author: Christophe Fraser
Author: Tanya Golubchik
Corporate Author: Oxford Virus Sequencing Analysis Group (OVSG)
Corporate Author: COVID-19 Genomics UK (COG-UK) consortium

Download statistics

Downloads from ePrints over the past year. Other digital versions may also be available to download e.g. from the publisher's website.

View more statistics

Library staff additional information
Atom RSS 1.0 RSS 2.0

Contact ePrints Soton: eprints@soton.ac.uk

ePrints Soton supports OAI 2.0 with a base URL of http://eprints.soton.ac.uk/cgi/oai2

This repository has been built using EPrints software, developed at the University of Southampton, but available to everyone to use.

We use cookies to ensure that we give you the best experience on our website. If you continue without changing your settings, we will assume that you are happy to receive cookies on the University of Southampton website.

×