Application of a targeted-enrichment methodology for full-genome sequencing of Dengue 1-4, Chikungunya and Zika viruses directly from patient samples
Application of a targeted-enrichment methodology for full-genome sequencing of Dengue 1-4, Chikungunya and Zika viruses directly from patient samples
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DOI：
10.1371/journal.pntd.0007184
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发表时间：
2019-04-01
影响因子：
3.8
通讯作者：
Sessions, October Michael
中科院分区：
文献类型：
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作者：
Kamaraj, Uma Sangumathi;Tan, Jun Hao;Sessions, October Michael
近年来，由登革热病毒1-4型、寨卡病毒和基孔肯雅病毒引起的流行病的频率呈上升趋势，主要是由于不受控制的城市化、人口流动及其共同媒介埃及伊蚊和白纹伊蚊的地理传播。这些病毒的感染具有相似的临床表现，使其难以诊断;这在世界上这些病毒高度流行的地区尤其困难。在这项研究中，我们提出了一个有针对性的富集方法，同时测序这些病毒的完整基因组直接从临床样本。此外，我们还开发了一个定制的计算工具（BaitMaker）来设计这些富集诱饵。该方法在捕获不同序列的能力方面是稳健的，并且适合于大规模流行病学研究。我们将这种方法应用于两个大型队列：2009-2015年登革热流行期间在斯里兰卡科隆博进行的发热研究（n = 170）和2016年新加坡寨卡病毒爆发期间进行的另一项研究（n = 162）。这些研究的结果表明，我们能够覆盖这些队列中样本的平均97.04%-0.67%的全病毒基因组。我们还显示了一个DENV 3/ZIKV共感染患者的检测，其中我们恢复了两种病毒的完整基因组。
The frequency of epidemics caused by Dengue viruses 1-4, Zika virus and Chikungunya viruses have been on an upward trend in recent years driven primarily by uncontrolled urbanization, mobility of human populations and geographical spread of their shared vectors, Aedes aegypti and Aedes albopictus. Infections by these viruses present with similar clinical manifestations making them challenging to diagnose; this is especially difficult in regions of the world hyperendemic for these viruses. In this study, we present a targeted-enrichment methodology to simultaneously sequence the complete viral genomes for each of these viruses directly from clinical samples. Additionally, we have also developed a customized computational tool (BaitMaker) to design these enrichment baits. This methodology is robust in its ability to capture diverse sequences and is amenable to large-scale epidemiological studies. We have applied this methodology to two large cohorts: a febrile study based in Colombo, Sri Lanka taken during the 2009-2015 dengue epidemic (n = 170) and another taken during the 2016 outbreak of Zika virus in Singapore (n = 162). Results from these studies indicate that we were able to cover an average of 97.04% 0.67% of the full viral genome from samples in these cohorts. We also show detection of one DENV3/ZIKV co-infected patient where we recovered full genomes for both viruses.