Abstract
Since the reemergence of St. Louis Encephalitis (SLE) Virus (SLEV) in the Southwest United States, identified during the 2015 outbreak in Arizona, SLEV has been seasonally detected within Culex spp. populations throughout the Southwest United States. Previous work revealed the 2015 outbreak was caused by an importation of SLEV genotype III, which had only been detected previously in Argentina. However, little is known about when the importation occurred or the transmission and genetic dynamics since its arrival into the Southwest. In this study, we sought to determine whether the annual detection of SLEV in the Southwest is due to enzootic cycling or new importations. To address this question, we analyzed 174 SLEV genomes (142 sequenced as part of this study) using Bayesian phylogenetic analyses to estimate the date of arrival into the American Southwest and characterize the underlying population structure of SLEV. Phylogenetic clustering showed that SLEV variants circulating in Maricopa and Riverside counties form two distinct populations with little evidence of inter-county transmission since the onset of the outbreak. Alternatively, it appears that in 2019, Yuma and Clark counties experienced annual importations of SLEV that originated in Riverside and Maricopa counties. Finally, the earliest representatives of SLEV genotype III in the Southwest form a polytomy that includes both California and Arizona samples. We propose that the initial outbreak most likely resulted from the importation of a population of SLEV genotype III variants, perhaps in multiple birds, possibly multiple species, migrating north in 2013, rather than a single variant introduced by one bird.
Highlights
Bayesian Tip-association Significance testing (BaTS) uses three statistics, the Association Index (AI; Wang et al, 2001), Fitch parsimony score (PS; Fitch, 1971), and the maximum exclusive single-state clade size (MC; Parker et al, 2008), to determine if character states are clustered more frequently within a phylogeny than would be expected due to chance. We focused this analysis on the Clade 2 Maricopa County-derived genomes, 75 genomes in total, as that is the only location where St. Louis Encephalitis Virus (SLEV) positive mosquito pools were distributed among both Culex quinquefasciatus and Cx. tarsalis populations
The formation of sister clades is indicative of multiple migration events into the Southwest, the time of arrival needs to be addressed for each clade independently
Our study revealed that the introduction of SLEV into the Southwest occurred between September 2011 and May 2014, but went undetected until the 2015 outbreak
Summary
St. Louis Encephalitis Virus (SLEV) is the causative agent of the disease St. Louis Encephalitis (SLE). 80% of clinical cases result in encephalitis, of which 5–20% is fatal (Reisen, 2003). SLEV was not discovered until 1933, after a viral outbreak in St. Louis, Missouri resulted in 1,095 reported cases, including 201 fatalities (Webster and Fite, 1933). Genotypes I and II have caused over 50 SLEV outbreaks in the United States and southern Canada, resulting in ~10,000 reported encephalitis cases and more than 1,000 fatalities (Webster and Fite, 1933; Day, 2001)
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