Identification of Viruses in Cases of Pediatric Acute Encephalitis and Encephalopathy Using Next-Generation Sequencing

Abstract

Acute encephalitis/encephalopathy is a severe neurological syndrome that is occasionally associated with viral infection. Comprehensive virus detection assays are desirable because viral pathogens have not been identified in many cases. We evaluated the utility of next-generation sequencing (NGS) for detecting viruses in clinical samples of encephalitis/encephalopathy patients. We first determined the sensitivity and quantitative performance of NGS by comparing the NGS-determined number of sequences of human herpesvirus-6 (HHV-6) in clinical serum samples with the HHV-6 load measured using real-time PCR. HHV-6 was measured as it occasionally causes neurologic disorders in children. The sensitivity of NGS for detection of HHV-6 sequences was equivalent to that of real-time PCR, and the number of HHV-6 reads was significantly correlated with HHV-6 load. Next, we investigated the ability of NGS to detect viral sequences in 18 pediatric patients with acute encephalitis/encephalopathy of unknown etiology. A large number of Coxsackievirus A9 and mumps viral sequences were detected in the cerebrospinal fluid of 2 and 1 patients, respectively. In addition, Torque teno virus and Pepper mild mottle viral sequences were detected in the sera of one patient each. These data indicate that NGS is useful for detection of causative viruses in patients with pediatric encephalitis/encephalopathy.

Identification of potential pathogenic viruses in patients with acute myocarditis using next‐generation sequencing

“…Recently, NGS has been applied in the field of infectious diseases, and its utility has been indicated . We previously applied NGS to detect viral sequences in clinical samples of patients with encephalitis and hepatitis . Thus, we anticipated that viruses associated with myocarditis could be detected from sera by NGS.…”

“…Recently, next‐generation sequencing (NGS) has enabled the comprehensive detection of pathogenic microorganisms, and this method has been applied in the field of infectious diseases . We previously analyzed sera of encephalitis, fulminant hepatitis, and bloodstream infection with unknown etiology and identified viral and bacterial genomes of presumptive pathogens of the diseases . In this study, we comprehensively analyzed microorganisms using NGS in sera of patients with myocarditis to identify the potential pathogenic viruses.…”

Encephalitis diagnosis using metagenomics: application of next generation sequencing for undiagnosed cases

“…The aforementioned studies also included only samples for which primary routine diagnostic testing using standard methods was negative therefore the utility of NGS as a first-line test cannot be assessed. A higher diagnostic yield was reported where specimens were tested using metagenomics as a firstline screening tool; 19% using whole CSF 41 and 30% using brain biopsies. 45 The use of brain tissue rather than CSF may increase diagnostic yield.…”

“…Five reports included testing multiple cases of encephalitis; in these the diagnostic yield was 0% (0/36), 7 1.6% (2/125), 29 6% (4/62), 37 19% (3/16) 41 and 30% (3/10). 45 The first three studies with low diagnostic yield of 0-6% tested only CSF supernatant which is cell-free, therefore only cell free viruses or cell-free microbial nucleic acid can be detected; moreover CSF often contains a lower pathogen load then brain biopsies and so pathogen detection is more challenging.…”

The Secret Lives of Human Herpes Virus 6 (HHV-6)

“…immune surveillance of the brain, and which is much more rapidly fatal than MS, will serve as a catalyst for increased political pressure. If the reasoning presented above remains insufficient to convince clinicians to perform these trials, then the proof of the proposed multiple roles of HHV-6 may have to await transcriptome sequencing studies, a drawnout, back-to-front approach [62,63]. This paper is also written for the patient, to promote more intensive and effective treatment for HHV-6-related demyelinating diseases.…”