Use of base excision sequence scanning for detection of genetic variationsin St. Louis encephalitis virus isolates

Twenty-two isolates of St. Louis encephalitis (SLE) virus of various geogra phical origins (Brazil, Argentina, Panama, Texas, Missouri, Maryland, Calif ornia, and Florida) were examined for genetic variation by the base excisio n sequence scanning (BESS T-scan) method. A fragment was amplified in the e nvelope gene with the forward primer labeled in the PCR The BESS T-scan met hod determined different clusters according to the profiles generated for t he isolates and successfully grouped the isolates according to their geogra phical origins. Two major clusters, the North American cluster (cluster A) and the South and Central American cluster (cluster B), were defined. Two s ubgroups, the Texas-California subgroup (subgroup Al) and the Missouri-Mary land-Florida subgroup (subgroup A2), were distinguished within group A. Sim ilarly, group B strains were subclustered to a South American subgroup (sub group B1) and a Central American subgroup (subgroup B2). These results were consistent with those obtained by DNA sequencing analysis. The ability of the BESS T-scan method to discriminate between strains that present with hi gh degrees of nucleotide sequence similarity indicated that this method pro vides reliable results and multiple applications for other virus families. The method has proven to be suitable for phylogenetic comparison and molecu lar epidemiology studies and may be an alternative to DNA sequencing.