Zoll Jan, Rahamat-Langendoen Janette, Ahout Inge, de Jonge Marien I, Jans Jop, Huijnen Martijn A, Ferwerda Gerben, Warris Adilia, Melchers Willem J G
Department of Medical Microbiology, Radboudumc, Nijmegen, The Netherlands.
Department of Medical Microbiology, Radboudumc, Nijmegen, The Netherlands.
J Clin Virol. 2015 May;66:6-11. doi: 10.1016/j.jcv.2015.02.010. Epub 2015 Feb 18.
Acute respiratory tract infections (RTI) cause substantial morbidity during childhood, and are responsible for the majority of pediatric infectious diseases. Although most acute RTI are thought to be of viral origin, viral etiology is still unknown in a significant number of cases.
Multiplexed whole genome sequencing (WGS) was used for virome determination directly on clinical samples as proof of principle for the use of deep sequencing techniques in clinical diagnosis of viral infections.
WGS was performed with nucleic acids from sputum and nasopharyngeal aspirates from four pediatric patients with known respiratory tract infections (two patients with human rhinovirus, one patient with human metapneumovirus and one patient with respiratory syncytial virus), and from four pediatric patients with PCR-negative RTI, and two control samples.
Viral infections detected by routine molecular diagnostic methods were confirmed by WGS; in addition, typing information of the different viruses was generated. In three out of four samples from pediatric patients with PCR-negative respiratory tract infections and the two control samples, no causative viral pathogens could be detected. In one sample from a patient with PCR-negative RTI, rhinovirus type-C was detected. Almost complete viral genomes could be assembled and in all cases virus species could be determined.
Our study shows that, in a single run, viral pathogens can be detected and characterized, providing information for clinical assessment and epidemiological studies. We conclude that WGS is a powerful tool in clinical virology that delivers comprehensive information on the viral content of clinical samples.
急性呼吸道感染（RTI）在儿童期会导致大量发病，并且是大多数儿科传染病的病因。尽管大多数急性RTI被认为是病毒源性的，但在相当数量的病例中病毒病因仍不明确。
采用多重全基因组测序（WGS）直接对临床样本进行病毒组测定，作为深度测序技术用于病毒感染临床诊断的原理验证。
对来自4名已知呼吸道感染的儿科患者（2名人鼻病毒患者、1名人间偏肺病毒患者和1名呼吸道合胞病毒患者）的痰液和鼻咽抽吸物中的核酸，以及来自4名PCR检测阴性的RTI儿科患者的核酸和2份对照样本进行WGS。
通过WGS证实了常规分子诊断方法检测到的病毒感染；此外，还生成了不同病毒的分型信息。在4名PCR检测阴性的呼吸道感染儿科患者的样本中有3份以及2份对照样本中，未检测到致病性病毒病原体。在1名PCR检测阴性的RTI患者的样本中，检测到了C型鼻病毒。几乎可以组装出完整的病毒基因组，并且在所有病例中都可以确定病毒种类。
我们的研究表明，一次检测就能检测到病毒病原体并对其进行表征，为临床评估和流行病学研究提供信息。我们得出结论，WGS是临床病毒学中的一种强大工具，可提供有关临床样本病毒含量的全面信息。
