Fatal Human Infection with Evidence of Infection Variation of Eastern Equine Encephalitis Virus, Alabama, USA, 2019

Eastern equine encephalitis virus (EEEV) is an arbovirus in the family Togaviridae, genus Alphavirus, found in North America and associated with freshwater/hardwood swamps in the Atlantic, Gulf Coast, and Great Lakes regions. EEEV disease in humans is rare but causes substantial illness and death. To investigate the molecular epidemiology and microevolution of EEEV from a fatal case in Alabama, USA, in 2019, we used next-generation sequencing of serum and cerebrospinal fluid (CSF). Phylogenetic inference indicated that the infecting strain may be closely related to isolates from Florida detected during 2010-2014, suggesting potential seeding from Florida. EEEV detected in serum displayed a higher degree of variability with more single-nucleotide variants than that detected in the CSF. These data refine our knowledge of EEEV molecular epidemiologic dynamics in the Gulf Coast region and demonstrate potential quasispecies bottlenecking within the central nervous system of a human host.

Automated summary

This study investigated the molecular epidemiology and microevolution of EEEV from a fatal case in Alabama, USA in 2019, revealing a potential seeding of the infecting strain from Florida. It also found that EEEV detected in serum displayed higher variability with more single-nucleotide variants than that detected in the CSF. These findings enhance our understanding of EEEV molecular epidemiology dynamics in the Gulf Coast region and demonstrate potential quasispecies bottlenecking within the central nervous system of a human host.