Performance of metagenomic next-generation sequencing for the diagnosis of viral meningoencephalitis in a resource-limited setting
| Autor: | Xutao Deng, Nguyen Thi Thu Hong, Nguyen Thi Hoang Mai, Nguyen Van Vinh Chau, H. Rogier van Doorn, Eric Delwart, Ho Dang Trung Nghia, Nguyen To Anh, Le Van Tan, Le Nguyen Truc Nhu, Nguyen Hoan Phu, Tran Tan Thanh, Guy E. Thwaites |
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| Jazyk: | angličtina |
| Rok vydání: | 2020 |
| Předmět: |
0301 basic medicine
viruses MinION Mumps virus Dengue virus medicine.disease_cause Virus 03 medical and health sciences 0302 clinical medicine Major Article medicine 030212 general & internal medicine nanopore metagenomics business.industry Varicella zoster virus meningoencephalitis Meningoencephalitis Japanese encephalitis medicine.disease Virology 3. Good health 030104 developmental biology Infectious Diseases Herpes simplex virus Oncology Enterovirus next-generation sequencing business |
| Zdroj: | Open Forum Infectious Diseases |
| Popis: | Background 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. Methods We assessed the performance of mNGS in the 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 polymerase chain reaction (PCR). As a complementary analysis, 6 viral PCR-positive samples were analyzed using MinION-based metagenomics. Results Routine diagnosis could identify a virus in 15 (22.7%) patients, including herpes simplex virus (HSV; n = 7) and varicella zoster virus (VZV; n = 1) by PCR, and mumps virus (n = 4), dengue virus (DENV; n = 2), and Japanese encephalitis virus (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 it detected DENV and JEV in none of the positive CSF. Additionally, mNGS detected enteroviruses in 7 patients of unknown cause. Metagenomic MinION-Nanopore sequencing could detect a virus in 5/6 PCR-positive CSF samples, including HSV in 1 CSF sample that was negative by mNGS, suggesting that the sensitivity of MinION is comparable with that of mNGS/PCR. Conclusions In a single assay, metagenomics could accurately detect a wide spectrum of neurotropic viruses in the CSF of meningoencephalitis patients. Further studies are needed 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. |
| Databáze: | OpenAIRE |
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