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

[41] Within-Host Evolution of SARS-CoV-2 in a B-Cell Depleted Patient With Successful Treatment
Baek, Yae Jee
Park, Gemma
Choi, Jun Yong
Kim, Eun Jin
Kim, Bryan Inho
Gwack, Jin
Jung, Ji Ye
JOURNAL OF KOREAN MEDICAL SCIENCE, 2023, 38 (22)
[42] First case of within-host co-infection of different SARS-CoV-2 variants in Ecuador
Fernandez-Cadena, J. C.
Carvajal, M.
Munoz, E.
Prado-Vivar, B.
Marquez, S.
Proano, S.
Bayas, R.
Guadalupe, J. J.
Becerra-Wong, M.
Gutierrez, B.
Morey-Leon, G.
Trueba, G.
Grunauer, M.
Barragan, V.
Rojas-Silva, P.
Andrade-Molina, D.
Cardenas, P.
NEW MICROBES AND NEW INFECTIONS, 2022, 48
[43] Comparative analysis of within-host diversity among vaccinated COVID-19 patients infected with different SARS-CoV-2 variants
Al-Khatib, Hebah A.
Smatti, Maria K.
Ali, Fatma H.
Zedan, Hadeel T.
Thomas, Swapna
Ahmed, Muna N.
El-kahlout, Reham A.
Al Bader, Mashael A.
Elgakhlab, Dina
Coyle, Peter V.
Abu-Raddad, Laith J.
Al Thani, Asma A.
Yassine, Hadi M.
ISCIENCE, 2022, 25 (11)
[44] Effect of ACE2 receptor and CTL response on within-host dynamics of SARS-CoV-2 infection
Elaiw, Ahmed M.
Alsulami, Amani S.
Hobiny, Aatef D.
JOURNAL OF MATHEMATICS AND COMPUTER SCIENCE-JMCS, 2024, 33 (03): : 298 - 325
[45] Case reports of persistent SARS-CoV-2 infection outline within-host viral evolution in immunocompromised patients
Ruotolo, Luca
Silenzi, Silvia
Mola, Beatrice
Ortalli, Margherita
Lazzarotto, Tiziana
Rossini, Giada
VIROLOGY JOURNAL, 2024, 21 (01)
[46] Dynamics of a within-host HIV/SARS-CoV-2 co-infection model with two intracellular delays
Hajri, Youssra
Amine, Saida
MATHEMATICS AND COMPUTERS IN SIMULATION, 2025, 232 : 160 - 191
[47] Prevention of host-to-host transmission by SARS-CoV-2 vaccines
Mostaghimi, Darius
Valdez, Caroline N.
Larson, Haleigh
Kalinich, Chaney C.
Iwasaki, Akiko
LANCET INFECTIOUS DISEASES, 2022, 22 (02): : E52 - E58
[48] Host Diversity and Potential Transmission Pathways of SARS-CoV-2 at the Human-Animal Interface
Hedman, Hayden D.
Krawczyk, Eric
Helmy, Yosra A.
Zhang, Lixin
Varga, Csaba
PATHOGENS, 2021, 10 (02): : 1 - 28
[49] Within-host evolution of SARS-CoV-2: how often are de novo mutations transmitted from symptomatic infections?
Korosec, Chapin S.
Wahl, Lindi M.
Heffernan, Jane M.
VIRUS EVOLUTION, 2024, 10 (01)
[50] A mathematical model of the within-host kinetics of SARS-CoV-2 neutralizing antibodies following COVID-19 vaccination
dePillis, Lisette
Caffrey, Rebecca
Chen, Ge
Dela, Mark D.
Eldevik, Leif
McConnell, Joseph
Shabahang, Shahrokh
Varvel, Stephen A.
JOURNAL OF THEORETICAL BIOLOGY, 2023, 556

← 1 2 3 4 5 →