Viral Metagenomic Analysis of Cerebrospinal Fluid from Patients with Acute Central Nervous System Infections of Unknown Origin, Vietnam

Abstract

Central nervous system (CNS) infection is a serious neurologic condition, although the etiology remains unknown in >50% of patients. We used metagenomic next-generation sequencing to detect viruses in 204 cerebrospinal fluid (CSF) samples from patients with acute CNS infection who were enrolled from Vietnam hospitals during 2012-2016. We detected 8 viral species in 107/204 (52.4%) of CSF samples. After virus-specific PCR confirmation, the detection rate was lowered to 30/204 (14.7%). Enteroviruses were the most common viruses detected (n = 23), followed by hepatitis B virus (3), HIV (2), molluscum contagiosum virus (1), and gemycircularvirus (1). Analysis of enterovirus sequences revealed the predominance of echovirus 30 (9). Phylogenetically, the echovirus 30 strains belonged to genogroup V and VIIb. Our results expanded knowledge about the clinical burden of enterovirus in Vietnam and underscore the challenges of identifying a plausible viral pathogen in CSF of patients with CNS infections.

Keywords: Vietnam; central nervous system infection; enterovirus; meningitis/encephalitis; next-generation sequencing; viral metagenomics; viruses.

Figure 1

Flowchart overview of diagnostic results for study of patients with suspected central nervous system infections admitted to 4 of 7 provincial hospitals, Vietnam, December 2012–October 2016. Inset map indicates places where samples were collected (red dots).

Figure 2

Number of cerebrospinal fluid samples with detected viruses by metagenomic next-generation sequencing and then confirmed by virus-specific PCR or reverse-transcription PCR, Vietnam, December 2012–October 2016. Samples were collected from patients with suspected central nervous system infection. For human papillomavirus, confirmatory testing was not performed because of the unavailability of a PCR assay.

Figure 3

Temporal distribution of enterovirus cases detected from cerebrospinal fluid samples of patients with suspected central nervous system infection by metagenomic next-generation sequencing and RT-PCR, Vietnam, December 2012–October 2016. Enterovirus RT-PCR results were obtained from the original study. RT-PCR, reverse transcription PCR. A) Combined data from 3 provinces; B) data from Hue province; C) data from Khanh Hoa province; D) data from Dak Lak province.

Figure 4

Phylogenetic tree of 298 complete viral protein 1 sequences of echovirus 30 (876 nt) isolated from cerebrospinal fluid samples of patients with suspected central nervous system infection, Vietnam, December 2012–October 2016. The inner color strip indicates 7 genogroups. The outer colorstrip indicates different countries of echovirus 30 isolates included in the tree. The outgroup is echovirus 21 Farina.