Abbreviations APACHE II score: Acute Physiology and Chronic Health Evaluation II; ARDS: Acute respiratory distress syndrome; CAP: Community-acquired pneumonia; CURB-65: Confusion, urea, respiration, blood pressure and age ≥65 years; EDTA: Ethylenediaminetetraacetic acid: ELISA: Enzyme-Linked ImmunoSorbent Assay; FACS flow: Fluorescence-Activated Cell Sorting, flow cytometry; FITC: Fluorescein isothiocyanate; HMGB-1: High-mobility group box 1; MFI: Mean fluorescence intensity; NF-κB: Nuclear factor-kappa B; PSI: Pneumonia Severity Index; RAGE: Receptor for advanced glycation end products; sRAGE: Soluble RAGE. Virus Identification in Unknown Tropical Febrile Illness Cases Using Deep Sequencing Dengue virus is an emerging infectious agent that infects an estimated 50–100 million people annually worldwide, yet current diagnostic practices cannot detect an etiologic pathogen in ∼40% of dengue-like illnesses. Metagenomic approaches to pathogen detection, such as viral microarrays and deep sequencing, are promising tools to address emerging and non-diagnosable disease challenges. In this study, we used the Virochip microarray and deep sequencing to characterize the spectrum of viruses present in human sera from 123 Nicaraguan patients presenting with dengue-like symptoms but testing negative for dengue virus. We utilized a barcoding strategy to simultaneously deep sequence multiple serum specimens, generating on average over 1 million reads per sample. We then implemented a stepwise bioinformatic filtering pipeline to remove the majority of human and low-quality sequences to improve the speed and accuracy of subsequent unbiased database searches. By deep sequencing, we were able to detect virus sequence in 37% (45/123) of previously negative cases. These included 13 cases with Human Herpesvirus 6 sequences. Other samples contained sequences with similarity to sequences from viruses in the Herpesviridae, Flaviviridae, Circoviridae, Anelloviridae, Asfarviridae, and Parvoviridae families. In some cases, the putative viral sequences were virtually identical to known viruses, and in others they diverged, suggesting that they may derive from novel viruses. These results demonstrate the utility of unbiased metagenomic approaches in the detection of known and divergent viruses in the study of tropical febrile illness. Viral infections pose a significant global health burden, especially in the developing world where most infectious disease deaths occur in children and are commonly due to preventable or treatable agents. Effective diagnostic and surveillance tools are crucial for reducing disability-adjusted-life-years (DALYs) due to infectious agents and for bolstering elimination and treatment programs [1] . Previously unrecognized and novel pathogens continually emerge due to globalization, climate change, and environmental encroachment, and pose important diagnostic challenges [2, 3] .