Division of Infectious Diseases, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN 37232, USA.
Division of Infectious Diseases, Department of Pediatrics, Vanderbilt University Medical Center, Nashville, TN 37232, USA.
Cell Rep Methods. 2021 Oct 25;1(6). doi: 10.1016/j.crmeth.2021.100091.
We developed a metatranscriptomics method that can simultaneously capture the respiratory virome, microbiome, and host response directly from low biomass samples. Using nasal swab samples, we capture RNA virome with sufficient sequencing depth required to assemble complete genomes. We find a surprisingly high frequency of respiratory syncytial virus (RSV) and coronavirus (CoV) in healthy children, and a high frequency of RSV-A and RSV-B co-detections in children with symptomatic RSV. In addition, we have identified commensal and pathogenic bacteria and fungi at the species level. Functional analysis revealed that was highly active in symptomatic RSV subjects. The host nasal transcriptome reveled upregulation of the innate immune system, anti-viral response and inflammasome pathway, and downregulation of fatty acid pathways in children with symptomatic RSV. Overall, we demonstrate that our method is broadly applicable to infer the transcriptome landscape of an infected system, surveil respiratory infections, and to sequence RNA viruses directly from clinical samples.
我们开发了一种宏转录组学方法，能够直接从低生物量样本中同时捕获呼吸病毒组、微生物组和宿主反应。我们使用鼻拭子样本，以足够的测序深度捕获 RNA 病毒组，从而组装完整的基因组。我们发现健康儿童中呼吸道合胞病毒（RSV）和冠状病毒（CoV）的频率高得惊人，症状性 RSV 儿童中 RSV-A 和 RSV-B 的共同检出率也很高。此外，我们还在种属水平上鉴定出了共生菌和致病菌。功能分析表明，在症状性 RSV 患者中，高度活跃。宿主鼻转录组显示，症状性 RSV 患儿的先天免疫系统、抗病毒反应和炎症小体途径上调，脂肪酸途径下调。总的来说，我们证明了我们的方法广泛适用于推断感染系统的转录组图谱、监测呼吸道感染以及直接从临床样本中测序 RNA 病毒。
