Products & Services


Nanopore sequencing offers advantages in all areas of research. Our offering includes DNA sequencing, as well as RNA and gene expression analysis and future technology for analysing proteins.

Learn about applications
View all Applications
News Explore

Performance of metagenomic next-generation sequencing for the diagnosis of viral meningoencephalitis in a resource limited setting


Date: 8th February 2020 | Source: Open Forum Infectious Diseases

Authors: Nguyen Thi Thu Hong, Nguyen To Anh, Nguyen Thi Hoang Mai, Ho Dang Trung Nghia, Le Nguyen Truc Nhu, Tran Tan Thanh, Nguyen Hoan Phu, Xutao Deng, H Rogier van Doorn, Nguyen Van Vinh Chau, Eric Delwart, Guy Thwaites, Le Van Tan.

Meningoencephalitis is a devastating disease worldwide. Current diagnosis fails to establish the cause in ≥50% of patients. Metagenomic next-generation sequencing (mNGS) has emerged as pan-pathogen assays for infectious-diseases diagnosis, but few studies have been conducted in resource-limited settings.

We assessed the performance of mNGS on cerebrospinal fluid (CSF) of 66 consecutively treated adults with meningoencephalitis in a tertiary referral hospital for infectious diseases in Vietnam, a resource-limited setting. All mNGS results were confirmed by viral specific PCRs. As a complementary analysis, six viral-PCR positive samples were analyzed using MinION-based metagenomics.

Routine diagnosis could identify a virus in 15 (22.7%) patients, including HSV (n=7) and VZV (n=1) by PCR, and mumps virus (n=4), DENV (n=2) and JEV (n=1) by serological diagnosis. mNGS detected HSV, VZV and mumps virus in 5/7, 1/1 and 1/4 of the CSF positive by routine assays, respectively, but DENV and JEV in none of the positive CSF. Additionally, mNGS detected enteroviruses in seven patients of unknown cause. Metagenomic MinION-nanopore sequencing could detect a virus in 5/6 PCR positive CSF samples, including HSV in one CSF negative by mNGS, suggesting that the sensitivity of MinION is comparable with that of mNGS/PCR.

In a single assay, metagenomics could accurately detect a wide spectrum of neurotropic viruses in CSF of meningoencephalitis patients. The study needed is to determine the value that real-time sequencing may contribute to the diagnosis and management of meningoencephalitis patients, especially in resource-limited settings where pathogen-specific assays are limited in number.

Read the full text Read the metagenomics white paper

Recommended for you

Open a chat to talk to our sales team