Application of next generation sequencing for the detection of human viral pathogens in clinical specimens.
Application of next generation sequencing for the detection of human viral pathogens in clinical specimens.
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DOI：
10.1016/j.jcv.2016.11.010
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发表时间：
2017-01
期刊：
影响因子：
--
通讯作者：
Chen J
中科院分区：
文献类型：
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作者：
Parker J;Chen J
下一代测序（NGS）是一项新技术，可用于广泛检测传染性病原体，并迅速成为临床实验室的重要平台。目前尚不清楚NGS将如何取代或加强传染病诊断中的金标准方法。探讨NGS技术在公共卫生实验室的可行性及应用，并与常规方法进行比较。使用Illumina MiSeq系统与其他常规病毒学方法一起使用典型的临床标本基质检测病毒病原体。分析了16份临床标本和2个CDC熟练度样本组（含17份标本）。在所有临床标本中均阳性鉴定出已知致病性病毒核酸，这与通过更常规的实验室方法获得的结果相关并建立在其基础上。测序深度范围从0.008X到319，基因组覆盖范围从0. 6%至99.9%。为了证实所述用于分析临床标本数据的方法，还提供了临床熟练度小组的结果。我们的研究结果揭示了临床标本中已知致病性病毒核酸的真正稀缺性。在本研究中，NGS在周转时间以及血清分型和耐药性方面的知识深度方面优于更传统的检测方法。
Next generation sequencing (NGS) is a new technology that can be used for broad detection of infectious pathogens and is rapidly becoming an essential platform in clinical laboratories. It is not known how NGS will displace or enhance gold standard methodologies in infectious disease diagnosis. To investigate the feasibility and application of NGS technology in public health laboratories and compare NGS technology with conventional methods. Illumina MiSeq system was used to detect viral pathogens alongside other conventional virology methods using typical clinical specimen matrices. Sixteen clinical specimens and two CDC proficiency panels containing seventeen specimens were analyzed. Known pathogenic viral nucleic acid was positively identified in all clinical specimens, correlating and building upon results obtained by more conventional laboratory methods. Sequencing depths ranged from 0.008X to 319 and genome coverage ranged from 0. 6% to 99.9%. To substantiate the described methods used to analyze data derived from clinical specimens, the results of a clinical proficiency panel are also presented. Our results reveal true scarcity of known pathogenic viral nucleic acids in clinical specimens. NGS outperforms more conventional detection methods in this study by turnaround time as well as the improved depth of knowledge in regards to serotyping and drug resistance.