Genomic epidemiology reveals multiple introductions of SARS-CoV-2 from mainland Europe into Scotland

被引：72

作者：

da Silva Filipe, Ana ^{[1
]}

Shepherd, James G. ^{[1
]}

Williams, Thomas ^{[2
]}

Hughes, Joseph ^{[1
]}

Aranday-Cortes, Elihu ^{[1
]}

Asamaphan, Patawee ^{[1
]}

Ashraf, Shirin ^{[1
]}

Balcazar, Carlos ^{[3
]}

Brunker, Kirstyn ^{[1
]}

Campbell, Alasdair ^{[4
]}

Carmichael, Stephen ^{[1
]}

Davis, Chris ^{[1
,5
]}

Dewar, Rebecca ^{[5
]}

Gallagher, Michael D. ^{[6
]}

Gunson, Rory ^{[7
,8
]}

Hill, Verity ^{[9
]}

Ho, Antonia ^{[1
]}

Jackson, Ben ^{[9
]}

James, Edward ^{[10
]}

Jesudason, Natasha ^{[1
]}

Johnson, Natasha ^{[1
]}

McWilliam Leitch, E. Carol ^{[1
]}

Li, Kathy ^{[1
]}

MacLean, Alasdair ^{[7
]}

Mair, Daniel ^{[1
]}

McAllister, David A. ^{[11
,12
]}

McCrone, John T. ^{[9
]}

McDonald, Sarah E. ^{[1
]}

McHugh, Martin P. ^{[5
,13
]}

Morris, A. Keith ^{[14
]}

Nichols, Jenna ^{[1
]}

Niebel, Marc ^{[1
]}

Nomikou, Kyriaki ^{[1
]}

Orton, Richard J. ^{[1
]}

O'Toole, Aine ^{[9
]}

Palmarini, Massimo ^{[1
]}

Parcell, Benjamin J. ^{[15
]}

Parr, Yasmin A. ^{[1
]}

Rambaut, Andrew ^{[9
]}

Rooke, Stefan ^{[8
]}

Shaaban, Sharif ^{[11
]}

Shah, Rajiv ^{[1
]}

Singer, Joshua B. ^{[1
]}

Smollett, Katherine ^{[1
]}

Starinskij, Igor ^{[7
]}

Tong, Lily ^{[1
]}

Sreenu, Vattipally B. ^{[1
]}

Wastnedge, Elizabeth ^{[5
]}

Holden, Matthew T. G. ^{[11
,13
]}

Robertson, David L. ^{[1
]}

机构：

[1] MRC Univ Glasgow, Ctr Virus Res CVR, Glasgow, Lanark, Scotland

[2] Univ Edinburgh, MRC Inst Genet & Mol Med, Edinburgh, Midlothian, Scotland

[3] Univ Edinburgh, Queens Med Res Inst, Edinburgh, Midlothian, Scotland

[4] Royal Hosp Children & Young People, Edinburgh, Midlothian, Scotland

[5] Royal Infirm Edinburgh NHS Trust, Virol Dept, Edinburgh, Midlothian, Scotland

[6] Univ Edinburgh, Roslin Inst, Edinburgh, Midlothian, Scotland

[7] Glasgow Royal Infirm, West Scotland Specialist Virol Ctr, Glasgow, Lanark, Scotland

[8] Univ Glasgow, Inst Infect Immun & Inflammat, Glasgow, Lanark, Scotland

[9] Univ Edinburgh, Inst Evolutionary Biol, Edinburgh, Midlothian, Scotland

[10] Borders Gen Hosp, Melrose, Scotland

[11] Publ Hlth Scotland, Glasgow, Lanark, Scotland

[12] Univ Glasgow, Inst Hlth & Wellbeing, Glasgow, Lanark, Scotland

[13] Univ St Andrews, Sch Med, St Andrews, Fife, Scotland

[14] Victoria Hosp, Kirkcaldy, Scotland

[15] Ninewells Hosp & Med Sch, Dundee, Scotland

[16] London Sch Hyg & Trop Med, Dept Clin Res, London, England

来源：

NATURE MICROBIOLOGY | 2021年 / 6卷 / 01期

基金：

英国医学研究理事会; 英国惠康基金;

关键词：

EPICENTER; VIRUS;

D O I：

10.1038/s41564-020-00838-z

中图分类号：

Q93 [微生物学];

学科分类号：

071005 ; 100705 ;

摘要：

Genomic epidemiology reveals multiple travel-related introductions of SARS-CoV-2 from mainland Europe into Scotland during the first wave of COVID-19. Coronavirus disease 2019 (COVID-19) was first diagnosed in Scotland on 1 March 2020. During the first month of the outbreak, 2,641 cases of COVID-19 led to 1,832 hospital admissions, 207 intensive care admissions and 126 deaths. We aimed to identify the source and number of introductions of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) into Scotland using a combined phylogenetic and epidemiological approach. Sequencing of 1,314 SARS-CoV-2 viral genomes from available patient samples enabled us to estimate that SARS-CoV-2 was introduced to Scotland on at least 283 occasions during February and March 2020. Epidemiological analysis confirmed that early introductions of SARS-CoV-2 originated from mainland Europe (the majority from Italy and Spain). We identified subsequent early outbreaks in the community, within healthcare facilities and at an international conference. Community transmission occurred after 2 March, 3 weeks before control measures were introduced. Earlier travel restrictions or quarantine measures, both locally and internationally, would have reduced the number of COVID-19 cases in Scotland. The risk of multiple reintroduction events in future waves of infection remains high in the absence of population immunity.

引用

页码：112 / +

页数：18

共 28 条

[1]

[Anonymous], 2020, PREP COR STEPP

[2]

[Anonymous], 2020, FOR OFF ADV ALL ESS

[3]

[Anonymous], 2020, COMM DIS THREAT REP

[4]

[Anonymous], 2020, LANCET MICROBE, V1, pe99, DOI [10.1016/S2666-5247(20)30054-9, DOI 10.1016/S2666-5247(20)30054-9]

[5] Measurably evolving pathogens in the genomic era [J].

Biek, Roman ;

Pybus, Oliver G. ;

Lloyd-Smith, James O. ;

Didelot, Xavier .

TRENDS IN ECOLOGY & EVOLUTION, 2015, 30 (06) :306-313

[6] Detection of 2019 novel coronavirus (2019-nCoV) by real-time RT-PCR (Publication with Expression of Concern) [J].

Corman, Victor M. ;

Landt, Olfert ;

Kaiser, Marco ;

Molenkamp, Richard ;

Meijer, Adam ;

Chu, Daniel K. W. ;

Bleicker, Tobias ;

Bruenink, Sebastian ;

Schneider, Julia ;

Schmidt, Marie Luisa ;

Mulders, Daphne G. J. C. ;

Haagmans, Bart L. ;

van der Veer, Bas ;

van den Brink, Sharon ;

Wijsman, Lisa ;

Goderski, Gabriel ;

Romette, Jean-Louis ;

Ellis, Joanna ;

Zambon, Maria ;

Peiris, Malik ;

Goossens, Herman ;

Reusken, Chantal ;

Koopmans, Marion P. G. ;

Drosten, Christian .

EUROSURVEILLANCE, 2020, 25 (03) :23-30

[7]

European Center for Disease Prevention and Control, 2020, OUTBR NOV COR DIS 20

[8] METHODS FOR COMPUTING WAGNER TREES [J].

FARRIS, JS .

SYSTEMATIC ZOOLOGY, 1970, 19 (01) :83-&

[9] The species Severe acute respiratory syndrome-related coronavirus: classifying 2019-nCoV and naming it SARS-CoV-2 [J].

Gorbalenya, Alexander E. ;

Baker, Susan C. ;

Baric, Ralph S. ;

de Groot, Raoul J. ;

Drosten, Christian ;

Gulyaeva, Anastasia A. ;

Haagmans, Bart L. ;

Lauber, Chris ;

Leontovich, Andrey M. ;

Neuman, Benjamin W. ;

Penzar, Dmitry ;

Perlman, Stanley ;

Poon, Leo L. M. ;

Samborskiy, Dmitry V. ;

Sidorov, Igor A. ;

Sola, Isabel ;

Ziebuhr, John .

NATURE MICROBIOLOGY, 2020, 5 (04) :536-544

[10] An amplicon-based sequencing framework for accurately measuring intrahost virus diversity using PrimalSeq and iVar [J].

Grubaugh, Nathan D. ;

Gangavarapu, Karthik ;

Quick, Joshua ;

Matteson, Nathaniel L. ;

De Jesus, Jaqueline Goes ;

Main, Bradley J. ;

Tan, Amanda L. ;

Paul, Lauren M. ;

Brackney, Doug E. ;

Grewal, Saran ;

Gurfield, Nikos ;

Van Rompay, Koen K. A. ;

Isern, Sharon ;

Michael, Scott F. ;

Coffey, Lark L. ;

Loman, Nicholas J. ;

Andersen, Kristian G. .

GENOME BIOLOGY, 2019, 20 (1)

← 1 2 3 →