Integrating host response analysis and VSITA metagenomic detection in cerebrospinal fluid from suspected encephalitis cases
10.3760/cma.j.issn.1003-9279.2019.03.002
- VernacularTitle: 应用宿主应答分析与VSITA宏基因组测序技术在疑似脑炎患者脑脊液中检出病原体
- Author:
Yi ZHANG
1
;
Yang LI
1
;
Mengjiie YANG
1
;
Hong ZHANG
2
;
Xuejun MA
1
Author Information
1. NHC Key Laboratory of Medical Virology and Viral Diseases, National Insitute of Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, China
2. Department of Microbiology, Hunan Provincial Center for Disease Control and Prevention, Changsha 410005, China
- Publication Type:Journal Article
- Keywords:
Encephalitis;
Virus sequence independent targeted amplification;
Metagenomic sequencing;
Host response;
Cytomegalovirus
- From:
Chinese Journal of Experimental and Clinical Virology
2019;33(3):231-235
- CountryChina
- Language:Chinese
-
Abstract:
Objective:To detect pathogens in clinical cerebrospinal fluid samples from 5 suspected encephalitis cases.
Methods:Five cerebrospinal samples were treated with both random and virus sequence independent targeted amplification(VSITA) method , followed by next-generation sequencing. Host trascriptome profiling combined with quantitative PCR were conducted to verify the detected pathogen.
Results:Cytomegalovirus(CMV) was detected in 3 cases. Quantitative PCR showed weakly positive result (Ct value: 30.23, 32.83, 34.08). The enhancement result of host infection pathway indicated CMV infection (P=0.213). Sequencing reads analysis showed better result in VSITA (P=0.096).
Conclusions:This is the first application of VSITA for cerebrospinal fluid samples. This enrichment method showed great potential while it needs further improvement. Consistency in gene expression detection between VSITA and random method makes it possible for host transcriptome profiling. Analysis result detected increase of CMV infection pathway in 3 positive cases, which further identified CMV infection in the 3 cases.
