Integrating host response analysis and VSITA metagenomic detection in cerebrospinal fluid from suspected encephalitis cases / 中华实验和临床病毒学杂志

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.