Identification of genetic variation among St. Louis encephalitis virus isolates, using single-strand conformation polymorphism analysis

A single-strand conformation polymorphism (SSCP) technique was developed fo r identification of genetic variation among 26 isolates of St. Louis enceph alitis (SLE) virus. A 750-bp portion of the envelope gene was amplified by reverse transcription-polymerase chain reaction (RT-PCR) and the products a nalyzed by SSCP. SSCP reliably identified genetic variation among the isola tes from the US, Central and South America. Closely related isolates from a smaller geographic area (Panama) were also distinguishable by SSCP. The se nsitivity of this technique was demonstrated by sequencing each of the isol ates used; SSCP was capable of discriminating between isolates that had as few as 1-6 nucleotide differences. These results indicate that SSCP has exc ellent potential as a tool to screen rapidly SLE virus isolates for genetic variation and could be incorporated into molecular epidemiology studies. ( C) 1999 Elsevier Science B.V. All rights reserved.