IFM Bioinformatics and Swedish e-Science Research Centre (SeRC), Linköping University, Linköping, Sweden.
PLoS One. 2012;7(2):e30875. doi: 10.1371/journal.pone.0030875. Epub 2012 Feb 15.
The human respiratory tract is heavily exposed to microorganisms. Viral respiratory tract pathogens, like RSV, influenza and rhinoviruses cause major morbidity and mortality from respiratory tract disease. Furthermore, as viruses have limited means of transmission, viruses that cause pathogenicity in other tissues may be transmitted through the respiratory tract. It is therefore important to chart the human virome in this compartment. We have studied nasopharyngeal aspirate samples submitted to the Karolinska University Laboratory, Stockholm, Sweden from March 2004 to May 2005 for diagnosis of respiratory tract infections. We have used a metagenomic sequencing strategy to characterize viruses, as this provides the most unbiased view of the samples. Virus enrichment followed by 454 sequencing resulted in totally 703,790 reads and 110,931 of these were found to be of viral origin by using an automated classification pipeline. The snapshot of the respiratory tract virome of these 210 patients revealed 39 species and many more strains of viruses. Most of the viral sequences were classified into one of three major families; Paramyxoviridae, Picornaviridae or Orthomyxoviridae. The study also identified one novel type of Rhinovirus C, and identified a number of previously undescribed viral genetic fragments of unknown origin.
人体的呼吸道与大量微生物频繁接触。呼吸道病毒病原体，如 RSV、流感病毒和鼻病毒，会导致严重的呼吸道疾病发病率和死亡率。此外，由于病毒的传播方式有限，可能会通过呼吸道传播引起其他组织病变的病毒。因此，了解呼吸道中的人类病毒组非常重要。我们研究了 2004 年 3 月至 2005 年 5 月间提交到瑞典斯德哥尔摩卡罗林斯卡大学实验室用于诊断呼吸道感染的鼻咽抽吸样本。我们采用宏基因组测序策略来对病毒进行特征分析，因为这种方法可以提供对样本最无偏倚的观察。病毒富集后通过 454 测序总共得到 703790 个读段，其中 110931 个读段通过自动分类管道被鉴定为病毒来源。对这 210 位患者的呼吸道病毒组进行快照分析，揭示了 39 种病毒和更多的病毒株。大多数病毒序列被分为三类：副黏液病毒科、小核糖核酸病毒科或正黏病毒科。该研究还鉴定出一种新型的鼻病毒 C，以及一些以前未描述过的、来源不明的新的病毒遗传片段。
