Application of Metagenomic NextGen Sequencing Technology to Identify Etiology of Fatal Acute Encephalitis Syndrome (AES) in Nepal

Rajeev Shrestha and colleagues at Dhulikhel Hospital, Kathmandu University in Nepal will apply metagenomic, next generation sequencing technology to identify causative pathogens of fatal acute encephalitis to improve diagnosis and treatment. Acute encephalitis syndrome (AES) annually affects over 100,000 individuals in low- and middle-income countries, causing substantial morbidity and mortality. It is a diverse disease caused by over 100 different pathogens, including viruses and parasites, making accurate diagnosis difficult, even in high-resource settings. This hinders prevention and treatment efforts, even though several effective vaccines exist. To better characterize the pathogens causing AES, particularly treatable and emerging ones, they will apply metagenomic, next generation sequencing technology to 60 banked cerebral spinal fluid samples collected from fatal acute encephalitis cases in Nepal as part of a nationwide AES surveillance program that covered 189 hospitals. They will validate and refine their technique using previously validated samples.