Geographically Distinct Circulation of Genotype II and III St. Louis Encephalitis Virus, Texas, USA, 2009–2024

We conducted a retrospective genomic surveillance study of St. Louis encephalitis virus (SLEV) in Texas, USA, to determine the genotypes circulating in the region. By using a custom tiled-amplicon assay with Oxford Nanopore sequencing, we generated 63 genomes from SLEV-positive mosquito pools and viral isolates collected during 2009-2024. Phylogenomic analysis revealed temporal overlap of genotype II and III circulation, but with distinct geographic segregation. Genotype II was confined to Gulf Coast counties with sustained local transmission, whereas genotype III was only in north and west Texas, but with persistent circulation and repeated introductions. We identified the earliest known US genotype III sequences, although their phylogenetic placement leaves the entry point of genotype III into the United States unresolved. Our findings emphasize the need for clinical vigilance in West Texas, where SLEV and West Nile virus co-circulate, and suggest the Gulf Coast may be buffered against foreign genotype introduction.