SARS-CoV-2 within-host diversity and transmission

被引：304

作者：

Lythgoe, Katrina A. ^{[1
,2
]}

Hall, Matthew ^{[1
]}

Ferretti, Luca ^{[1
]}

de Cesare, Mariateresa ^{[1
,3
]}

MacIntyre-Cockett, George ^{[1
,3
]}

Trebes, Amy ^{[3
]}

Andersson, Monique ^{[4
,5
]}

Otecko, Newton ^{[1
]}

Wise, Emma L. ^{[6
,7
]}

Moore, Nathan ^{[6
]}

Lynch, Jessica ^{[6
]}

Kidd, Stephen ^{[6
]}

Cortes, Nicholas ^{[6
,8
]}

Mori, Matilde ^{[9
]}

Williams, Rebecca ^{[6
]}

Vernet, Gabrielle ^{[6
]}

Justice, Anita ^{[4
]}

Green, Angie ^{[3
]}

Nicholls, Samuel M. ^{[10
]}

Ansari, M. Azim ^{[11
]}

Abeler-Dorner, Lucie ^{[1
]}

Moore, Catrin E. ^{[1
]}

Peto, Timothy E. A. ^{[4
,12
]}

Eyre, David W. ^{[4
,13
]}

Shaw, Robert ^{[4
]}

Simmonds, Peter ^{[11
]}

Buck, David ^{[3
]}

Todd, John A. ^{[3
]}

Connor, Thomas R. ^{[14
,15
]}

Ashraf, Shirin ^{[16
]}

Filipe, Ana da Silva ^{[16
]}

Shepherd, James ^{[16
]}

Thomson, Emma C. ^{[16
]}

Bonsall, David ^{[1
,3
,4
]}

Fraser, Christophe ^{[1
,3
,17
]}

Golubchik, Tanya ^{[1
,2
]}

机构：

[1] Univ Oxford, Big Data Inst, Nuffield Dept Med, Old Rd Campus, Oxford OX3 7LF, England

[2] Univ Oxford, Dept Zool, Oxford OX1 3SZ, England

[3] Univ Oxford, Wellcome Ctr Human Genet, NIHR Biomed Res Ctr, Nuffield Dept Med, Old Rd Campus, Oxford OX3 7BN, England

[4] Oxford Univ Hosp NHS Fdn Trust, John Radcliffe Hosp, Oxford OX3 9DU, England

[5] Stellenbosch Univ, Div Med Virol, Stellenbosch, South Africa

[6] Hampshire Hosp NHS Fdn Trust, Basingstoke & North Hampshire Hosp, Basingstoke RG24 9NA, Hants, England

[7] Univ Surrey, Sch Biosci & Med, Guildford GU2 7XH, Surrey, England

[8] Gibraltar Hlth Author, Gibraltar, Gibraltar

[9] Univ Southampton, Sch Med, Southampton SO17 1BJ, Hants, England

[10] Univ Birmingham, Inst Microbiol & Infect, Birmingham B15 2TT, W Midlands, England

[11] Univ Oxford, Peter Medawar Bldg Pathogen Res, Oxford OX1 3SY, England

[12] Univ Oxford, John Radcliffe Hosp, Nuffield Dept Med, Oxford OX3 9DU, England

[13] Univ Oxford, Big Data Inst, Nuffield Dept Publ Hlth, Old Rd Campus, Oxford OX3 7FL, England

[14] Publ Hlth Wales Microbiol, Pathogen Genom Unit, Cardiff CF10 4BZ, Wales

[15] Cardiff Univ, Sch Biosci, Cardiff CF10 3AX, S Glam, Wales

[16] MRC Univ Glasgow Ctr Virus Res, Glasgow G61 1QH, Lanark, Scotland

[17] Wellcome Sanger Inst, Cambridge CB10 1SA, England

来源：

SCIENCE | 2021年 / 372卷 / 6539期

基金：

英国惠康基金; 英国医学研究理事会;

关键词：

VIRUS; BOTTLENECKS; INFECTION; MUTATIONS; ALIGNMENT; IMPACT;

D O I：

10.1126/science.abg0821

中图分类号：

O [数理科学和化学]; P [天文学、地球科学]; Q [生物科学]; N [自然科学总论];

学科分类号：

07 ; 0710 ; 09 ;

摘要：

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.

引用

页码：256 / +

页数：44

共 50 条

[31] Global stability of a within-host SARS-CoV-2/cancer model with immunity and diffusion
Elaiw, A. M.
Al Agha, A. D.
Alshaikh, M. A.
INTERNATIONAL JOURNAL OF BIOMATHEMATICS, 2022, 15 (02)
[32] Global analysis of within-host SARS-CoV-2/HIV coinfection model with latency
A. M. Elaiw
A. D. Al Agha
S. A. Azoz
E. Ramadan
The European Physical Journal Plus, 137
[33] A quantitative model used to compare within-host SARS-CoV-2, MERS-CoV, and SARS-CoV dynamics provides insights into the pathogenesis and treatment of SARS-CoV-2
Kim, Kwang Su
Ejima, Keisuke
Iwanami, Shoya
Fujita, Yasuhisa
Ohashi, Hirofumi
Koizumi, Yoshiki
Asai, Yusuke
Nakaoka, Shinji
Watashi, Koichi
Aihara, Kazuyuki
Thompson, Robin N.
Ke, Ruian
Perelson, Alan S.
Iwami, Shingo
Roberts, Roland G.
Roberts, Roland G.
Roberts, Roland G.
PLOS BIOLOGY, 2021, 19 (03)
[34] Within-host dynamics of SARS-CoV-2 infection: A systematic review and meta-analysis
Du, Zhanwei
Wang, Shuqi
Bai, Yuan
Gao, Chao
Lau, Eric H. Y.
Cowling, Benjamin J.
TRANSBOUNDARY AND EMERGING DISEASES, 2022, 69 (06) : 3964 - 3971
[35] Within-host delay differential model for SARS-CoV-2 kinetics with saturated antiviral responses
Dehingia, Kaushik
Das, Anusmita
Hincal, Evren
Hosseini, Kamyar
El Din, Sayed M.
MATHEMATICAL BIOSCIENCES AND ENGINEERING, 2023, 20 (11) : 20025 - 20049
[36] Within-host evolutionary dynamics and tissue compartmentalization during acute SARS-CoV-2 infection
Farjo, Mireille
Koelle, Katia
Martin, Michael A.
Gibson, Laura L.
Walden, Kimberly K. O.
Rendon, Gloria
Fields, Christopher J.
Alnaji, Fadi G.
Gallagher, Nicholas
Luo, Chun Huai
Mostafa, Heba H.
Manabe, Yukari C.
Pekosz, Andrew
Smith, Rebecca L.
Mcmanus, David D.
Brooke, Christopher B.
JOURNAL OF VIROLOGY, 2024, 98 (01)
[37] Modeling and Stability Analysis of Within-Host IAV/SARS-CoV-2 Coinfection with Antibody Immunity
Elaiw, Ahmed M.
Alsulami, Raghad S.
Hobiny, Aatef D.
MATHEMATICS, 2022, 10 (22)
[38] Within-host models of SARS-CoV-2: What can it teach us on the biological factors driving virus pathogenesis and transmission?
Prague, Melanie
Alexandre, Marie
Thiebaut, Rodolphe
Guedj, Jeremie
ANAESTHESIA CRITICAL CARE & PAIN MEDICINE, 2022, 41 (02)
[39] Disentangling the dynamical underpinnings of differences in SARS-CoV-2 pathology using within-host ecological models
Metcalf, C. Jessica E.
Grenfell, Bryan T.
Graham, Andrea L.
PLOS PATHOGENS, 2020, 16 (12)
[40] Different Within-Host Viral Evolution Dynamics in Severely Immunosuppressed Cases with Persistent SARS-CoV-2
Perez-Lago, Laura
Aldamiz-Echevarria, Teresa
Garcia-Martinez, Rita
Perez-Latorre, Leire
Herranz, Marta
Sola-Campoy, Pedro
Suarez-Gonzalez, Julia
Martinez-Laperche, Carolina
Comas, Inaki
Gonzalez-Candelas, Fernando
Catalan, Pilar
Munoz, Patricia
Garcia de Viedma, Dario
BIOMEDICINES, 2021, 9 (07)

← 1 2 3 4 5 →