Rapid identification of flaviviruses based on conserved NS5 gene sequences

Two conserved regions in the sequence of the NS5 gene of Flaviviruses were identified. Primers were designed from the consensus sequence of these regions and were used in a reverse transcription/polymerase chain reaction (RT/PCR) to amplify a region of the central european tick-borne encephalitis virus Kumlinge NS5 gene. The authenticity of the amplified fragment was confirmed by nucleotide sequencing. A band of the expected size was also obtained when this RT/PCR was applied to 13 other flaviviral RNAs. This method may be useful for characterisation of the NS5 genes of flaviviruses and as a potential pan-flavivirus diagnostic tool.