ve-SEQ: Robust, unbiased enrichment for streamlined detection and whole-genome sequencing of HCV and other highly diverse pathogens.
ve-SEQ: Robust, unbiased enrichment for streamlined detection and whole-genome sequencing of HCV and other highly diverse pathogens.
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DOI：
10.12688/f1000research.7111.1
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发表时间：
2015
期刊：
影响因子：
--
通讯作者：
Bowden R
中科院分区：
文献类型：
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作者：
Bonsall D;Ansari MA;Ip C;Trebes A;Brown A;Klenerman P;Buck D;STOP-HCV Consortium;Piazza P;Barnes E;Bowden R
常规获得的高深度病毒序列数据将允许敏感地检测可能危及艾滋病毒或丙型肝炎病毒（HCV）治疗的耐药性相关变异。我们引入了ve-SEQ，这是一种高通量方法，用于序列特异性富集和全病毒基因组的表征，与参考序列的差异高达20%，灵敏度比直接测序高1000倍。HCV的极端遗传多样性使我们实现了一种算法，用于高效设计寡核苷酸探针面板，以捕获一组定义靶标中的任何序列，而不会出现可检测到的偏差。ve-SEQ能够在一次实验中有效地检测和测序任何HCV基因组，包括混合物和宿主内变异，比标准扩增方法具有更大的序列多样性耐受性，比宏基因组测序具有更高的灵敏度，这些特征直接适用于其他病原体或任意目标生物群体，允许在许多情况下将敏感检测与测序相结合。
The routine availability of high-depth virus sequence data would allow the sensitive detection of resistance-associated variants that can jeopardize HIV or hepatitis C virus (HCV) treatment. We introduce ve-SEQ, a high-throughput method for sequence-specific enrichment and characterization of whole-virus genomes at up to 20% divergence from a reference sequence and 1,000-fold greater sensitivity than direct sequencing. The extreme genetic diversity of HCV led us to implement an algorithm for the efficient design of panels of oligonucleotide probes to capture any sequence among a defined set of targets without detectable bias. ve-SEQ enables efficient detection and sequencing of any HCV genome, including mixtures and intra-host variants, in a single experiment, with greater tolerance of sequence diversity than standard amplification methods and greater sensitivity than metagenomic sequencing, features that are directly applicable to other pathogens or arbitrary groups of target organisms, allowing the combination of sensitive detection with sequencing in many settings.