Real-time, portable genome sequencing for Ebola surveillance.
Real-time, portable genome sequencing for Ebola surveillance.
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DOI：
10.1038/nature16996
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发表时间：
2016-02-11
期刊：
影响因子：
64.8
通讯作者：
Carroll MW
中科院分区：
文献类型：
--
作者：
Quick J;Loman NJ;Duraffour S;Simpson JT;Severi E;Cowley L;Bore JA;Koundouno R;Dudas G;Mikhail A;Ouédraogo N;Afrough B;Bah A;Baum JH;Becker-Ziaja B;Boettcher JP;Cabeza-Cabrerizo M;Camino-Sanchez A;Carter LL;Doerrbecker J;Enkirch T;Dorival IGG;Hetzelt N;Hinzmann J;Holm T;Kafetzopoulou LE;Koropogui M;Kosgey A;Kuisma E;Logue CH;Mazzarelli A;Meisel S;Mertens M;Michel J;Ngabo D;Nitzsche K;Pallash E;Patrono LV;Portmann J;Repits JG;Rickett NY;Sachse A;Singethan K;Vitoriano I;Yemanaberhan RL;Zekeng EG;Trina R;Bello A;Sall AA;Faye O;Faye O;Magassouba N;Williams CV;Amburgey V;Winona L;Davis E;Gerlach J;Washington F;Monteil V;Jourdain M;Bererd M;Camara A;Somlare H;Camara A;Gerard M;Bado G;Baillet B;Delaune D;Nebie KY;Diarra A;Savane Y;Pallawo RB;Gutierrez GJ;Milhano N;Roger I;Williams CJ;Yattara F;Lewandowski K;Taylor J;Rachwal P;Turner D;Pollakis G;Hiscox JA;Matthews DA;O'Shea MK;Johnston AM;Wilson D;Hutley E;Smit E;Di Caro A;Woelfel R;Stoecker K;Fleischmann E;Gabriel M;Weller SA;Koivogui L;Diallo B;Keita S;Rambaut A;Formenty P;Gunther S;Carroll MW
西非的埃博拉病毒疫情是有记录以来最大的，造成28,599例病例和11,299例死亡。病毒暴发中的基因组测序是可取的，以确定感染源的特征，以确定其进化速度、宿主适应的特征、识别和监测诊断目标以及对疫苗和治疗的反应。据估计，埃博拉病毒基因组在马科纳株中的替换率每年在每个地点0.87×10−3到1.42×10−3突变之间。这相当于每个基因组中有16到27个突变，这意味着在一场旷日持久的疫情中，序列分化得足够快，可以识别出不同的亚谱系。基因组测序提供了病原体进化的高分辨率视图，并越来越受到疫情监测的追捧。序列数据可以用来指导控制措施，但只有在结果产生得足够快以通知干预措施的情况下才能使用。由于缺乏本地测序能力，加上将样本运送到远程测序设施的实际困难，疫情期间的基因组监测一直是零星的。为了解决这个问题，我们设计了一种利用新型纳米孔DNA测序仪的基因组监测系统。2015年4月，该系统被装在标准的航空行李中运往几内亚，并用于对正在流行的疫情进行实时基因组监测。在这里，我们提供了2015年3月至10月期间收集的142个埃博拉病毒(EBOV)样本的序列数据和分析。我们能够在收到埃博拉阳性样本后不到24小时内得出结果，测序过程只需15-60分钟。我们表明，在资源有限的情况下，实时基因组监测是可能的，并可以迅速建立起来，以监测疫情。
The Ebola virus disease (EVD) epidemic in West Africa is the largest on record, responsible for >28,599 cases and >11,299 deaths . Genome sequencing in viral outbreaks is desirable in order to characterize the infectious agent to determine its evolutionary rate, signatures of host adaptation, identification and monitoring of diagnostic targets and responses to vaccines and treatments. The Ebola virus genome (EBOV) substitution rate in the Makona strain has been estimated at between 0.87 × 10−3 to 1.42 × 10−3 mutations per site per year. This is equivalent to 16 to 27 mutations in each genome, meaning that sequences diverge rapidly enough to identify distinct sub-lineages during a prolonged epidemic . Genome sequencing provides a high-resolution view of pathogen evolution and is increasingly sought-after for outbreak surveillance. Sequence data may be used to guide control measures, but only if the results are generated quickly enough to inform interventions . Genomic surveillance during the epidemic has been sporadic due to a lack of local sequencing capacity coupled with practical difficulties transporting samples to remote sequencing facilities . In order to address this problem, we devised a genomic surveillance system that utilizes a novel nanopore DNA sequencing instrument. In April 2015 this system was transported in standard airline luggage to Guinea and used for real-time genomic surveillance of the ongoing epidemic. Here we present sequence data and analysis of 142 Ebola virus (EBOV) samples collected during the period March to October 2015. We were able to generate results in less than 24 hours after receiving an Ebola positive sample, with the sequencing process taking as little as 15-60 minutes. We show that real-time genomic surveillance is possible in resource-limited settings and can be established rapidly to monitor outbreaks.