Mapping the clinical outcomes and genetic evolution of Ebola virus in Sierra Leone
Mapping the clinical outcomes and genetic evolution of Ebola virus in Sierra Leone
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DOI：
10.1172/jci.insight.88333
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发表时间：
2017-08-03
期刊：
影响因子：
8
通讯作者：
Cao, Wu-Chun
中科院分区：
文献类型：
--
作者：
Li, Tao;Yao, Hong-Wu;Cao, Wu-Chun
塞拉利昂是2013-2016年埃博拉病毒病（EVD）爆发期间西非受影响最严重的国家。以往的基因组监测研究揭示了埃博拉病毒（EBOV）的起源、多样性和进化动力学;然而，由于临床结果与EBOV遗传进化之间的相关性尚不清楚，因此有关EBOV序列的信息不足，特别是临床结果。在这里，我们收集和策划了一个全面的数据集，其中包括来自确诊EVD患者的514个EBOV基因组序列（包括60个先前未研究的序列），其中>87.5%具有居住信息和明确的临床结果。系统发育重建揭示了塞拉利昂的11个EBOV谱系。中位数加入单倍型网络表明，与致命结果相关的单倍型往往比具有活结果的单倍型更有助于EBOV在塞拉利昂的传播。时空分布的分析揭示了谱系独特的分布格局。不同的病毒谱系在爆发的同一阶段具有不同的病死率（CFR），这意味着具有SNP的几个谱系可能与CFR的增加/减少相关。这项研究提供了宝贵的数据集EBOV感染，并强调了潜在的SNPs进一步深入调查。
Sierra Leone was the most severely affected country in Western Africa during the 2013-2016 outbreak of Ebola virus disease (EVD). Previous genome surveillance studies have revealed the origin, diversity, and evolutionary dynamics of the Ebola virus (EBOV); however, the information regarding EBOV sequences is insufficient, especially the clinical outcomes, given that the correlation between the clinical outcomes and the genetic evolution of EBOV is still not clear. Here, we collected and curated a comprehensive data set that includes 514 EBOV genome sequences from patients with confirmed EVD (including 60 sequences not previously studied), >87.5% of which have residence information and definitive clinical outcomes. Phylogenetic reconstruction revealed 11 lineages of EBOV in Sierra Leone. The median-joining haplotype network showed that haplotypes that are associated with lethal outcomes tend to contribute more to the spread of the EBOV in Sierra Leone than those with live outcomes. Analyses of the spatial-temporal distribution unraveled the lineage-distinctive distribution patterns. Different viral lineages have different case fatality rates (CFRs) during the same stage of the outbreak, implying that several lineages featuring SNPs may correlate with increased/decreased CFRs. This study provides invaluable data sets of EBOV infection and highlights the potential SNPs for further in-depth investigation.