Rapid outbreak sequencing of Ebola virus in Sierra Leone identifies transmission chains linked to sporadic cases.
Rapid outbreak sequencing of Ebola virus in Sierra Leone identifies transmission chains linked to sporadic cases.
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DOI：
10.1093/ve/vew016
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发表时间：
2016-01
期刊：
影响因子：
5.3
通讯作者：
Cotten M
中科院分区：
文献类型：
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作者：
Arias A;Watson SJ;Asogun D;Tobin EA;Lu J;Phan MVT;Jah U;Wadoum REG;Meredith L;Thorne L;Caddy S;Tarawalie A;Langat P;Dudas G;Faria NR;Dellicour S;Kamara A;Kargbo B;Kamara BO;Gevao S;Cooper D;Newport M;Horby P;Dunning J;Sahr F;Brooks T;Simpson AJH;Groppelli E;Liu G;Mulakken N;Rhodes K;Akpablie J;Yoti Z;Lamunu M;Vitto E;Otim P;Owilli C;Boateng I;Okoror L;Omomoh E;Oyakhilome J;Omiunu R;Yemisis I;Adomeh D;Ehikhiametalor S;Akhilomen P;Aire C;Kurth A;Cook N;Baumann J;Gabriel M;Wölfel R;Di Caro A;Carroll MW;Günther S;Redd J;Naidoo D;Pybus OG;Rambaut A;Kellam P;Goodfellow I;Cotten M
为了结束西非已知最大规模的埃博拉病毒病（EVD）疫情并防止新的传播，需要对病例和接触者进行快速流行病学追踪。快速识别未知来源和传播链的能力是结束埃博拉病毒病流行的关键，在最近报告埃博拉病毒（EBOV）在幸存者中持续存在的背景下显得更加重要。对完整埃博拉病毒基因组进行系统发育分析可以提供有关任何新感染来源的重要信息。塞拉利昂中部的马特内埃博拉治疗中心建立了当地的深度测序设施。该设施包括所有湿实验室和计算资源，可将 EBOV 诊断样本快速处理成完整基因组序列。我们从塞拉利昂各地的埃博拉病毒病病例中产生了 554 个埃博拉病毒基因组。这些基因组提供了埃博拉病毒进化的详细描述，并促进了新埃博拉病毒病病例的系统发育追踪。重要的是，我们表明，关联的基因组和流行病学数据不仅可以支持接触者追踪，还可以识别涉及体液（包括精液）的非常规传播链。埃博拉病毒基因组快速测序与流行病学信息和整个疫情爆发期间的病毒序列综合数据库相结合，为公共卫生流行病控制工作提供了强大的工具。
To end the largest known outbreak of Ebola virus disease (EVD) in West Africa and to prevent new transmissions, rapid epidemiological tracing of cases and contacts was required. The ability to quickly identify unknown sources and chains of transmission is key to ending the EVD epidemic and of even greater importance in the context of recent reports of Ebola virus (EBOV) persistence in survivors. Phylogenetic analysis of complete EBOV genomes can provide important information on the source of any new infection. A local deep sequencing facility was established at the Mateneh Ebola Treatment Centre in central Sierra Leone. The facility included all wetlab and computational resources to rapidly process EBOV diagnostic samples into full genome sequences. We produced 554 EBOV genomes from EVD cases across Sierra Leone. These genomes provided a detailed description of EBOV evolution and facilitated phylogenetic tracking of new EVD cases. Importantly, we show that linked genomic and epidemiological data can not only support contact tracing but also identify unconventional transmission chains involving body fluids, including semen. Rapid EBOV genome sequencing, when linked to epidemiological information and a comprehensive database of virus sequences across the outbreak, provided a powerful tool for public health epidemic control efforts.