Unbiased Parallel Detection of Viral Pathogens in Clinical Samples by Use of a Metagenomic Approach
Unbiased Parallel Detection of Viral Pathogens in Clinical Samples by Use of a Metagenomic Approach
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DOI：
10.1128/jcm.00273-11
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发表时间：
2011-10-01
影响因子：
9.4
通讯作者：
Jin, Qi
中科院分区：
文献类型：
--
作者：
Yang, Jian;Yang, Fan;Jin, Qi
病毒性传染病是对公众健康的重大威胁，也是全世界最大的疾病负担之一。快速和准确地识别病毒因子对于疫情控制和估计区域疾病负担都至关重要。最近发展的宏基因组方法已被证明是同时检测病原体的有力工具。在这里，我们对基于短读的宏基因组方法在急性下呼吸道感染患者鼻咽吸入样本中病毒病原体分子检测中的能力进行了系统研究（n = 16）。利用超深测序的高通量和专用的数据解释方法，我们成功地从15份样本中鉴定出7种已知的呼吸道病毒因子，结果与传统PCR分析结果一致。我们还发现了一个常规PCR检测未发现的合并感染病例。利用宏基因组数据，对样本中检测丰度较高的病毒的11个草图基因组进行了重构，覆盖率为21.84% ~ 98.53%。我们的研究结果显示了基于短读的宏基因组方法对病毒病原体的准确和平行筛选的能力。尽管将该方法应用于临床样品存在一些固有的困难，包括缺乏控制，样品数量有限，高污染率，但我们的工作将促进这种前所未有的高通量方法进一步应用于临床样品。
Viral infectious diseases represent a major threat to public health and are among the greatest disease burdens worldwide. Rapid and accurate identification of viral agents is crucial for both outbreak control and estimating regional disease burdens. Recently developed metagenomic methods have proven to be powerful tools for simultaneous pathogen detection. Here, we performed a systematic study of the capability of the short-read-based metagenomic approach in the molecular detection of viral pathogens in nasopharyngeal aspirate samples from patients with acute lower respiratory tract infections (n = 16). Using the high-throughput capacity of ultradeep sequencing and a dedicated data interpretation method, we successfully identified seven species of known respiratory viral agents from 15 samples, a result that was consistent with results of conventional PCR assays. We also detected a coinfected case that was missed by regular PCR testing. Using the metagenomic data, 11 draft genomes of the abundantly detected viruses in the samples were reconstructed with 21.84% to 98.53% coverage. Our results show the power of the short-read-based metagenomic approach for accurate and parallel screening of viral pathogens. Although there are some inherent difficulties in applying this approach to clinical samples, including a lack of controls, limited specimen quantity, and high contamination rate, our work will facilitate further application of this unprecedented high-throughput method to clinical samples.