DETECTION OF WEST NILE VIRUS BY THE POLYMERASE CHAIN-REACTION AND ANALYSIS OF NUCLEOTIDE-SEQUENCE VARIATION

A polymerase chain reaction (PCR) assay was developed to rapidly detec t and identify West Nile (WN) virus. The RNA from seven isolates of WN virus from six countries and four other flaviviruses (Kunjin, Japanes e encephalitis, St. Louis encephalitis, and yellow fever viruses) was reverse-transcribed (RT) and amplified by PCR. The nucleotide sequence s of the amplified products were determined by a rapid, automated DNA sequencing method. The WN virus RT/PCR assay detected the target gene segment of isolates from both the African-Middle Eastern group and the Indian group with a sensitivity of approximately 0.05 pg of viral RNA . Kunjin virus was the only other flavivirus tested that produced a ba nd of the appropriate size. Five of seven WN virus isolates showed 92- 98% homology in the nucleotide sequence of their PCR products. The seq uence of one isolate was virtually identical to the published sequence of the Nigerian isolate (99.5% homology). No correlation was establis hed between the degree of nucleotide homology, geographic location, ti me of isolation, or source of the isolates.