Using Metagenomic NextGen Sequencing Technology to Determine Etiologies of Severe or Fatal Acute Encephalitis Syndrome in Nepal

Acute Encephalitis Syndrome (AES) is characterized by acute onset of fever and altered sensorium followed by rapidly worsening clinical condition and even death. The causative agents vary with season and geographic location, while the etiologies remain unknown in 68-75% of the cases. In Nepal, the cases of acute encephalitis syndrome are tested only for Japanese encephalitis, which constitutes about just 15% of the case globally. However, there could be several causative organisms, including vaccine preventable etiologies that cause acute encephalitis, which upon identification could direct public health efforts for prevention, including expanded use of vaccines or address gaps in vaccine coverage.

Study Duration: Phase I: 01/05/2019 – 29/02/2021
                              Phase II: 07/2022 – Present


This study employs metagenomic Next Generation Sequencing in exploration of infective etiologies behind acute encephalitis syndrome, in a low-and-middle-income setting.



From this study, two documented, causative agents were revealed through metagenomic next generation sequencing. We have concluded that there is dire need of implementing stringent collection procedures for sample collection, including proper process controls. We have also advocated that the investigation of disease of unknown etiologies, such as AES, through mNGS is useful in developing clinical management algorithms and break investigation. Additionally, we are planning for prospective investigation of CSF samples of subjects suffering from AES.


Team Members

Principal Investigator(s): Prof. Dr. Rajeev Shrestha

Co-Investigator(s): Dr. Dipesh Tamrakar, Dr. Biraj Man Karmacharya, Dr. Runa Jha

Project Coordinator/Molecular Biologist: Nishan Katuwal


Supported by: Bill and Melinda Gates Foundation

Collaborating Partners: Chan Zuckerberg Biohub (CZ Biohub), Chan Zuckerberg Initiative (CZI), USA and National Public Health Laboratory (NPHL), WHO-IPD, Nepal