Nucleic acid sequence-based amplification assays for rapid detection of West Nile and St. Louis encephalitis viruses

The development and application of nucleic acid sequence-based amplificatio n (NASBA) assays for the detection of West Nile (WN) and St. Louis encephal itis (SLE) viruses are reported. Two unique detection formats were develope d for the NASBA assays: a postamplification detection step with a virus-spe cific internal capture probe and electrochemiluminescence (NASBA-ECL assay) and a real-time assay with 6-carboxyfluorescein-labeled virus-specific mol ecular beacon probes (NASBA-beacon assay). The sensitivities and specificit ies of these NASBA assays were compared to those of a newly described stand ard reverse transcription (RT)-PCR and TaqMan assays for SLE virus and to a previously published TaqMan assay for WN virus. The NASBA assays demonstra ted exceptional sensitivities and specificities compared to those of virus isolation, the TaqMan assays, and standard RT-PCR, with the NASBA-beacon as say yielding results in less than 1 h. These assays should be of utility in the diagnostic laboratory to complement existing diagnostic testing method ologies and as a tool in conducting flavivirus surveillance in the United S tates.