Retrospective genomic surveillance of St. Louis encephalitis virus (SLEV) in Texas (2009–2024) analyzed 63 genomes from SLEV-positive mosquito pools and isolates using tiled-amplicon sequencing with Oxford Nanopore.
The study aimed to identify circulating genotypes and their geographic distribution. Phylogenomic results show temporal overlap of genotypes II and III in Texas, with distinct geographic segregation: genotype II restricted to Gulf Coast counties with sustained local transmission, while genotype III occurred in north and West Texas, exhibiting persistent circulation and repeated introductions.
The analysis identified the earliest US genotype III sequences within the dataset, but the entry point of genotype III into the United States remains unresolved based on phylogenetic placement. SLEV activity in Texas has historically been higher along the Gulf Coast, with declines following West Nile virus (WNV) emergence; in this study, SLEV detection persisted in pockets across the state.
The authors highlight clinical vigilance in West Texas, where SLEV and WNV co-circulate, and suggest the Gulf Coast may be comparatively buffered against foreign genotype introduction.
CDC Emerging Infectious Diseases Journal published a clinical update in Infectious Disease on 31 Mar 2026.
The item focuses on Geographically Distinct Circulation of Genotype II and III St.
Louis Encephalitis Virus, Texas, USA, 2009–2024.
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