Newly developed TaqMan assay to detect West Nile viruses in a wide range of viral strains.

*Corresponding author: Mailing address: Yokohama City Institute of Health, Takigashira 1-2-17, Isogo-ku, Yokohama City, Kanagawa 235-0012, Japan. Tel: +81-45-754-9804, Fax: +81-45-754-2210, E-mail: [email protected] In the United States during 2003, 9,862 people were reported to be infected with West Nile virus (WNV) to the Centers for Disease Control and Prevention, and 264 of these people died of related encephalitis and meningitis (http://www.cdc.gov/ncidod/dvbid/westnile/surv&control CaseCount03_detailed.htm). There is the possibility of WNV infection even in Japan in the near future. Genetically, WNV can be divided into two lineages. NY99, prevalent in the United States in a 1999 survey of avian and mosquito samples, belongs to lineage 1 (1). Lanciotti et al. (2) developed a TaqMan Reverse Transcriptase (RT)-PCR assay based on the sequence of the NY99 strain. The 3 ́NC primers and probe assay detects 0.1 PFU/5 μl of sample of NY99 strain and reacts with other six WNV strains. Two main WNV strains, g2266 (lineage 1) and FCG (lineage 2), are available in local public laboratories in Japan. However, they are genetically distinct from the NY99 strain. The 3 ́NC primers and probe assay cannot detect the FCG and g2266 strains used as respective control strains in real time polymerase chain reaction (real time PCR) in a Japanese local laboratory. It is thus necessary to develop new primers and probe sets to detect various WNV strains in order to screen avian and mosquito samples. We developed a new TaqMan RT-PCR assay to detect both