Rapid implementation of SARS-CoV-2 sequencing to investigate cases of health-care associated COVID-19: a prospective genomic surveillance study

被引：255

作者：

Meredith, Luke W. ^{[1
]}

Hamilton, William L. ^{[2
,3
]}

Warne, Ben ^{[2
,3
]}

Houldcroft, Charlotte J. ^{[2
]}

Hosmillo, Myra ^{[1
]}

Jahun, Aminu S. ^{[1
]}

Curran, Martin D. ^{[4
]}

Parmar, Surendra ^{[4
]}

Caller, Laura G. ^{[1
,5
]}

Caddy, Sarah L. ^{[2
,6
]}

Khokhar, Fahad A. ^{[2
,6
]}

Yakovleva, Anna ^{[1
]}

Hall, Grant ^{[1
]}

Feltwell, Theresa ^{[2
]}

Forrest, Sally ^{[2
,6
]}

Sridhar, Sushmita ^{[2
,6
,7
]}

Weekes, Michael P. ^{[2
,6
]}

Baker, Stephen ^{[2
,6
]}

Brown, Nicholas ^{[4
]}

Moore, Elinor ^{[3
]}

Popay, Ashley ^{[8
]}

Roddick, Iain ^{[8
]}

Reacher, Mark ^{[8
]}

Gouliouris, Theodore ^{[3
,4
]}

Peacock, Sharon J. ^{[2
,9
]}

Dougan, Gordon ^{[2
,6
]}

Torok, M. Estee ^{[2
,3
]}

Goodfellow, Ian ^{[1
]}

机构：

[1] Univ Cambridge, Dept Pathol, Cambridge CB2 0QQ, England

[2] Univ Cambridge, Dept Med, Cambridge CB2 0QQ, England

[3] Cambridge Univ Hosp Natl Hlth Serv Fdn Trust, Cambridge, England

[4] Publ Hlth England Clin Microbiol & Publ Hlth Lab, Cambridge, England

[5] Francis Crick Inst, London, England

[6] Cambridge Inst Therapeut Immunol & Infect Dis, Cambridge, England

[7] Wellcome Sanger Inst, Hinxton, England

[8] Publ Hlth England, Natl Infect Serv, Field Serv, Field Epidemiol, Cambridge, England

[9] Publ Hlth England, Natl Infect Serv, London, England

来源：

LANCET INFECTIOUS DISEASES | 2020年 / 20卷 / 11期

基金：

英国科研创新办公室;

关键词：

REAL-TIME; VIRUS; OUTBREAKS; ZIKA;

D O I：

10.1016/S1473-3099(20)30562-4

中图分类号：

R51 [传染病];

学科分类号：

100401 ;

摘要：

Background The burden and influence of health-care associated severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infections is unknown. We aimed to examine the use of rapid SARS-CoV-2 sequencing combined with detailed epidemiological analysis to investigate health-care associated SARS-CoV-2 infections and inform infection control measures. Methods In this prospective surveillance study, we set up rapid SARS-CoV-2 nanopore sequencing from PCR-positive diagnostic samples collected from our hospital (Cambridge, UK) and a random selection from hospitals in the East of England, enabling sample-to-sequence in less than 24 h. We established a weekly review and reporting system with integration of genomic and epidemiological data to investigate suspected health-care associated COVID-19 cases. Findings Between March 13 and April 24, 2020, we collected clinical data and samples from 5613 patients with COVID-19 from across the East of England. We sequenced 1000 samples producing 747 high-quality genomes. We combined epidemiological and genomic analysis of the 299 patients from our hospital and identified 35 clusters of identical viruses involving 159 patients. 92 (58%) of 159 patients had strong epidemiological links and 32 (20%) patients had plausible epidemiological links. These results were fed back to clinical, infection control, and hospital management teams, leading to infection-control interventions and informing patient safety reporting. Interpretation We established real-time genornic surveillance of SARS-CoV-2 in a UK hospital and showed the benefit of combined genomic and epidemiological analysis for the investigation of health-care associated COVID-19. This approach enabled us to detect cryptic transmission events and identify opportunities to target infection-control interventions to further reduce health-care associated infections. Our findings have important implications for national public health policy as they enable rapid tracking and investigation of infections in hospital and community settings. Copyright (C) 2020 Elsevier Ltd. All rights reserved.

引用

页码：1263 / 1272

页数：10

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