St. Louis Encephalitis Virus in the Southwestern United States: A Phylogeographic Case for a Multi-Variant Introduction Event

Chase L. Ridenour, Jill Cocking, Samuel Poidmore, Daryn Erickson, Breezy Brock, Michael Valentine, Chandler C. Roe, Steven J. Young, Jennifer A. Henke, Kim Y. Hung, Jeremy Wittie, Elene Stefanakos, Chris Sumner, Martha Ruedas, Vivek Raman, Nicole Seaton, William Bendik, Heidie M. Hornstra O’Neill, Krystal Sheridan, Heather CentnerDarrin Lemmer, Viacheslav Fofanov, Kirk Smith, James Will, John Townsend, Jeffrey T. Foster, Paul S. Keim, David M. Engelthaler, Crystal M. Hepp

Research output: Contribution to journalArticlepeer-review

5 Scopus citations


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.

Original languageEnglish (US)
Article number667895
JournalFrontiers in Genetics
StatePublished - Jun 8 2021


  • Culex mosquitoes
  • St. Louis encephalitis virus
  • genomics
  • phylogenetic analysis

ASJC Scopus subject areas

  • Molecular Medicine
  • Genetics
  • Genetics(clinical)


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