Rapid implementation of SARS-CoV-2 sequencing to investigate cases of health-care associated COVID-19: a prospective genomic surveillance study.
Rapid implementation of SARS-CoV-2 sequencing to investigate cases of health-care associated COVID-19: a prospective genomic surveillance study.
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DOI：
10.1016/s1473-3099(20)30562-4
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发表时间：
2020-11
期刊：
影响因子：
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通讯作者：
Goodfellow I
中科院分区：
文献类型：
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作者：
Meredith LW;Hamilton WL;Warne B;Houldcroft CJ;Hosmillo M;Jahun AS;Curran MD;Parmar S;Caller LG;Caddy SL;Khokhar FA;Yakovleva A;Hall G;Feltwell T;Forrest S;Sridhar S;Weekes MP;Baker S;Brown N;Moore E;Popay A;Roddick I;Reacher M;Gouliouris T;Peacock SJ;Dougan G;Török ME;Goodfellow I
卫生保健相关的严重急性呼吸综合征冠状病毒2（SARS-CoV-2）感染的负担和影响尚不清楚。我们的目的是检查使用快速SARS-CoV-2测序结合详细的流行病学分析，以调查卫生保健相关的SARS-CoV-2感染，并告知感染控制措施。在这项前瞻性监测研究中，我们对从我们医院（英国剑桥）收集的PCR阳性诊断样本和从英格兰东部医院随机选择的样本进行了快速SARS-CoV-2纳米孔测序，使样本测序时间不到24小时。我们建立了一个每周审查和报告系统，整合了基因组和流行病学数据，以调查疑似医疗相关的COVID-19病例。在2020年3月13日至4月24日期间，我们收集了来自英格兰东部的5613名COVID-19患者的临床数据和样本。我们对1000个样本进行了测序，产生了747个高质量的基因组。我们结合了对我院299名患者的流行病学和基因组分析，发现了35个相同病毒簇，涉及159名患者。159例患者中有92例（58%）有很强的流行病学联系，32例（20%）患者有合理的流行病学联系。这些结果被反馈给临床、感染控制和医院管理团队，从而导致感染控制干预措施，并为患者安全报告提供信息。我们在英国一家医院建立了SARS-CoV-2的实时基因组监测，并显示了基因组和流行病学分析相结合对调查医疗保健相关COVID-19的益处。这种方法使我们能够检测到神秘的传播事件，并确定有针对性的感染控制干预措施，以进一步减少卫生保健相关的感染。我们的研究结果对国家公共卫生政策具有重要意义，因为它们可以快速跟踪和调查医院和社区环境中的感染。COVID-19英国基因组学（由英国研究与创新、国家健康研究所、威康桑格研究所支持）、威康信托基金会、医学科学院和健康基金会以及国家健康研究所剑桥生物医学研究中心。
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. 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. 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. We established real-time genomic 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. COVID-19 Genomics UK (supported by UK Research and Innovation, the National Institute of Health Research, the Wellcome Sanger Institute), the Wellcome Trust, the Academy of Medical Sciences and the Health Foundation, and the National Institute for Health Research Cambridge Biomedical Research Centre.