Multiple genotypes of St. Louis encephalitis virus (Flaviviridae: Flavivirus) circulate in Harris County, Texas.

St. Louis encephalitis (SLE) is endemic in Harris County, Texas. The disease is a public health concern in Houston, the largest city in Harris County, and in the state. Consequently, intensive surveillance for SLE virus in local mosquito populations is carried out by the Harris County Mosquito Control Division each year. In this study, we examined genetic variation among SLE isolates obtained during routine virus surveillance over a 13-year time period (1986-1999). St. Louis encephalitis virus isolates were tested for genetic variation using reverse transcription-polymerase chain reaction followed by single-strand conformation polymorphism (SSCP). The results indicated that multiple genotypes of the virus circulate in Harris County. During several years, the genotypes were restricted in their location, i.e., each general area within the county had a specific genotype of the virus. In other years, the various genotypes were widely distributed throughout the county. The presence of multiple distinct genotypes suggests that viruses with different biological characteristics may be circulating in Harris County, and that discrete foci of SLE virus activity occur simultaneously.