Detection of West Nile virus and Japanese encephalitis virus using real-time PCR with a probe common to both viruses.

A diagnostic method to distinguish between West Nile virus (WNV) and Japanese encephalitis virus (JEV) based on fluorogenic real-time polymerase chain reaction (TaqMan) assays was developed. To detect WNV and JEV with a single probe, a probe was designed to correspond to sequences in the core protein region that are shared by both viruses. The specificity of this assay depended on the primer sets used, which were specific to the target virus sequences: the primer set for WNV could detect only WNV strains and the primer set for JEV could detect only JEV strains. The assays were tested by detection of viruses from experimentally infected animal tissues. The method described in this study will be useful for the simultaneous discrimination of WNV and JEV in areas where JEV is endemic, such as East Asia.