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首页> 外文期刊>Journal of Clinical Microbiology >Unbiased Detection of Respiratory Viruses by Use of RNA Sequencing-Based Metagenomics: a Systematic Comparison to a Commercial PCR Panel
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Unbiased Detection of Respiratory Viruses by Use of RNA Sequencing-Based Metagenomics: a Systematic Comparison to a Commercial PCR Panel

机译：通过使用基于RNA测序的基因组学对呼吸道病毒进行无偏检测：与商业PCR专家组的系统比较

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Current infectious disease molecular tests are largely pathogen specific, requiring test selection based on the patient's symptoms. For many syndromes caused by a large number of viral, bacterial, or fungal pathogens, such as respiratory tract infections, this necessitates large panels of tests and has limited yield. In contrast, next-generation sequencing-based metagenomics can be used for unbiased detection of any expected or unexpected pathogen. However, barriers for its diagnostic implementation include incomplete understanding of analytical performance and complexity of sequence data analysis. We compared detection of known respiratory virus-positive (n = 42) and unselected (n = 67) pediatric nasopharyngeal swabs using an RNA sequencing (RNA-seq)-based metagenomics approach and Taxonomer, an ultrarapid, interactive, web-based metagenomics data analysis tool, with an FDA-cleared respiratory virus panel (RVP; GenMark eSensor). Untargeted metagenomics detected 86% of known respiratory virus infections, and additional PCR testing confirmed RVP results for only 2 (33%) of the discordant samples. In unselected samples, untargeted metagenomics had excellent agreement with the RVP (93%). In addition, untargeted metagenomics detected an additional 12 viruses that were either not targeted by the RVP or missed due to highly divergent genome sequences. Normalized viral read counts for untargeted metagenomics correlated with viral burden determined by quantitative PCR and showed high intrarun and interrun reproducibility. Partial or full-length viral genome sequences were generated in 86% of RNA-seq-positive samples, allowing assessment of antiviral resistance, strain-level typing, and phylogenetic relatedness. Overall, untargeted metagenomics had high agreement with a sensitive RVP, detected viruses not targeted by the RVP, and yielded epidemiologically and clinically valuable sequence information.
机译：当前的传染病分子测试主要是针对病原体的，需要根据患者的症状进行测试选择。对于由大量病毒，细菌或真菌病原体引起的许多综合症，例如呼吸道感染，这需要进行大量的检测，并且产量有限。相反，基于下一代测序的宏基因组学可用于任何预期或意外病原体的无偏检测。但是，其诊断实施的障碍包括对分析性能的不完全了解和序列数据分析的复杂性。我们使用基于RNA测序（RNA-seq）的宏基因组学比较了已知的呼吸道病毒阳性（ n = 42）和未选择的（ n = 67）儿科鼻咽拭子的检测方法和Taxonomer，一种基于Web的超快速，交互式，宏基因组学数据分析工具，具有FDA批准的呼吸道病毒检测小组（RVP; GenMark eSensor）。未靶向的宏基因组学检测到86％的已知呼吸道病毒感染，另外的PCR测试证实了仅2个（33％）不一致样品的RVP结果。在未选择的样本中，未靶向的宏基因组学与RVP（93％）具有极好的一致性。此外，未靶向的宏基因组学还检测出另外12种病毒，这些病毒不是RVP靶向的，就是由于基因组序列差异很大而被遗漏了。非靶向宏基因组学的标准化病毒读取计数与定量PCR测定的病毒载量相关，显示出较高的运行内和运行间可重复性。在86％的RNA-seq阳性样品中产生了部分或全长的病毒基因组序列，可以评估其抗病毒抗性，株型分型和系统发育相关性。总体而言，未靶向的宏基因组学与敏感的RVP高度吻合，检测到未被RVP靶向的病毒，并获得了流行病学和临床上有价值的序列信息。

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