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

Holly R Hughes,J Erin Staples,Emily H Davis,Jason O Velez,Janeen Laven,Amy J Lambert,Carolyn V Gould,Amanda J Panella,Aaron C Brault

doi:10.3201/eid2707.210315

Abstract

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.

Highlights

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
We investigated the molecular epidemiology of EEEV sequences from 1 patient infected with EEEV in Alabama, an area with historically limited genetic information about EEEV
Serum was negative for IgM against La Crosse virus, Jamestown Canyon virus, Powassan virus, and EEEV; neutralizing antibodies against EEEV were not detected

Summary

Introduction

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 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. In North America, eastern equine encephalitis virus (EEEV) causes disease in equids, domestic birds, and humans [1,2]. In the New England region, cases of eastern equine encephalitis (EEE) resulting from EEEV infection in Author affiliation: Centers for Disease Control and Prevention, Fort. Phylogenetic studies have shown substantial genetic diversity among isolates of Madariaga virus, the virus most closely related to EEEV [11]. All methods followed manufacturer’s recommended protocols unless otherwise noted

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Conclusion