This study describes the use of the Virochip microarray and deep sequencing for the direct viral diagnosis of serum from cases of acute pediatric febrile illness in a tropical urban setting. Patient clinical data and serum samples were collected between 2005 and 2009 as part of an ongoing pediatric dengue study in Managua, Nicaragua [31] . Virochip and deep sequencing were performed on positive control samples and on 123 dengue virus-negative serum samples. Using these methods, viruses were detected in 45 of 123 (37%) previously negative samples. Sequences derived from known and apparently divergent viruses. The viruses identified in some of the cases are known to induce symptoms consistent with those observed, though the definitive causative agent of these infections remains to be determined.