Viral infections pose a significant health burden and remain a leading cause of global morbidity and mortality. Yet, identifying the causative pathogen remains challenging in several clinical syndromes. Viral metagenomic next-generation sequencing enables the systematic detection of a full spectrum of known and novel viral pathogens and has numerous advantages compared to conventional diagnostic tests.

Dengue virus infection is the most common arthropod-borne viral disease of humans, with an estimated 100 million clinical infections occurring annually worldwide. Dengue infection typically manifests clinically as dengue fever or more severe dengue shock syndrome. In dengue-endemic countries such as the Philippines actual number of dengue cases are underreported due to mild symptoms and low percentage of diagnostic tests.

Hospitalised dengue cases are also often misdiagnosed as other febrile illness. As hospital-based acute febrile illness study is currently be performed in the Philippines. This additional study will focus on employing metagenomic sequencing to determine the aetiology of febrile illness in severe hospitalised cases and those cases whom current diagnostic assays have yielded negative results. The spectrum of viruses found will be compared against conventional diagnostic methods and the feasibility of integrating such tools as part of public health surveillance efforts assessed.