Rapid identification of flavivirus using the polymerase chain reaction

A rapid and accurate detection and identification system was developed for flaviviruses that makes use of reverse transcription-polymerase chain reaction (RT-PCR). A primer pair (YF-1 and YF-3), which corresponds to the highly conserved sequence at 3' noncoding region among flaviviruses, was useful for identification of mosquito-borne flaviviruses. Nine sets of species specific primer pairs were also selected to identify and distinguish species, i.e., yellow fever, West Nile, Murray Valley encephalitis, Japanese encephalitis, St. Louis encephalitis and dengue type 1 to 4 viruses. This method required only two hours for completion using infected culture fluid, thus facilitating rapid identification of mosquito-borne flavivirus species.