Methods and compositions for detecting the presence of a pathogen are described. In particular, this document provides a method of detecting a pathogen-associated nucleic acid in a biological sample of a subject, where the method comprises using one or more unimolecular aptamer-based sensors comprising an aptamer-fluorophore complex and an amplification step to detect the pathogen-associated nucleic acid. Methods specific for detecting the presence of malaria and other mosquito-borne virus infections are also provided.