Western equine encephalitis virus: evolutionary analysis of a declining alphavirus based on complete genome sequences

Abstract

Western equine encephalitis virus (WEEV) is an arbovirus from the genus Alphavirus, family Togaviridae, which circulates in North America between birds and mosquitoes, occasionally causing disease in humans and equids. In recent decades, human infection has decreased dramatically; the last documented human case in North America occurred in 1994, and the virus has not been detected in mosquito pools since 2008. Because limited information exists regarding the evolution of WEEV, we analyzed the genomic sequences of 33 low-passage-number strains with diverse geographic and temporal distributions and performed comprehensive phylogenetic analyses. Our results indicated that WEEV is a highly conserved alphavirus with only approximately 5% divergence in its most variable genes. We confirmed the presence of the previously determined group A and B lineages and further resolved group B into three sublineages. We also observed an increase in relative genetic diversity during the mid-20th century, which correlates with the emergence and cocirculation of several group B sublineages. The estimated WEEV population size dropped in the 1990s, with only the group B3 lineage being sampled in the past 20 years. Structural mapping showed that the majority of substitutions in the envelope glycoproteins occurred at the E2-E2 interface. We hypothesize that an event occurred in the mid-20th century that resulted in the increased genetic diversity of WEEV in North America, followed by genetic constriction due to either competitive displacement by the B3 sublineage or stochastic events resulting from a population decline.

Importance: Western equine encephalitis virus (WEEV) has caused several epidemics that resulted in the deaths of thousands of humans and hundreds of thousands of equids during the past century. During recent decades, human infection decreased drastically and the virus has not been found in mosquito pools since 2008. Because limited information exists regarding the evolution of WEEV, we analyzed 33 complete genome sequences and conducted comprehensive phylogenetic analyses. We confirmed the presence of two major lineages, one of which diverged into three sublineages. Currently, only one of those sublineages is found circulating in nature. Understanding the evolution of WEEV over the past century provides a unique opportunity to observe an arbovirus that is in decline and to better understand what factors can cause said decline.

FIG 1

Maximum clade credibility tree based on 33 WEEV complete genomes. Numbers at nodes indicate posterior probabilities of ≥0.9. Grey bars at nodes indicate 95% confidence intervals of divergence dates, and the x axis represents time in years. The four distinct lineages, groups A and B1 to B3, are indicated. Nonsynonymous synapomorphic mutations are indicated on the tree based on their identified nodes of occurrence. Taxon/tip labels include year of isolation, strain name, and state where the virus was isolated.

FIG 2

Bayesian skyline plot of WEEV strains in North America between 1930 and 2005. The centerline represents the estimate for mean genetic variation in the population through time. The upper and lower dashed lines represent the 95% HPD.

FIG 3

Predicted E1-E2 WEEV trimers. (A to C) Mapping of all mutations on WEEV BFS932 surface compared to all WEEV strains. (A) Top view; (B) side view; (C) bottom view. (D to F) Mapping of all mutations on the WEEV BFS932 surface compared to WEEV Imperial181. (D) Top view; (E) side view; (F) bottom view. All mutations in the E1 protein are shown in yellow, and those from the E2 protein are shown in red. Amino acids 374 in E1 protein (magenta) and 23 in E2 protein (green) also are indicated.