Approximately one half of the suspected dengue cases testing negative by all four dengue diagnostic assays were included in the metagenomics analysis described here. 34 cases (pools 1-4, see below) corresponded to the subset of patients who presented within 4 days of symptom onset and who reported both fever or history of fever and rash. 89 of the samples (pool 5) were selected randomly from among the remaining samples. As positive controls, seven samples (pool 5) that had been clinically diagnosed as virus positive were included. The study protocol was reviewed and approved by the Institutional Review Boards (IRB) of the University of California, Berkeley, and of the Nicaraguan Ministry of Health.