TY - JOUR
T1 - St. Louis Encephalitis Virus in the Southwestern United States
T2 - A Phylogeographic Case for a Multi-Variant Introduction Event
AU - Ridenour, Chase L.
AU - Cocking, Jill
AU - Poidmore, Samuel
AU - Erickson, Daryn
AU - Brock, Breezy
AU - Valentine, Michael
AU - Roe, Chandler C.
AU - Young, Steven J.
AU - Henke, Jennifer A.
AU - Hung, Kim Y.
AU - Wittie, Jeremy
AU - Stefanakos, Elene
AU - Sumner, Chris
AU - Ruedas, Martha
AU - Raman, Vivek
AU - Seaton, Nicole
AU - Bendik, William
AU - Hornstra O’Neill, Heidie M.
AU - Sheridan, Krystal
AU - Centner, Heather
AU - Lemmer, Darrin
AU - Fofanov, Viacheslav
AU - Smith, Kirk
AU - Will, James
AU - Townsend, John
AU - Foster, Jeffrey T.
AU - Keim, Paul S.
AU - Engelthaler, David M.
AU - Hepp, Crystal M.
N1 - Funding Information:
This work would not have been possible without the contributions of SLEV-positive mosquito pools from Maricopa County Environmental Services Vector Control Division, Coachella Valley Mosquito and Vector Control District, Yuma County Pest Abatement District, and Southern Nevada Health District. The laboratory equipment and space that were critical for the processing of the SLEV-positive mosquito pools was provided by The Pathogen and Microbiome Institute. The sequencing of the SLEV genomes was completed at Translational Genomics Research Institute North. The high-performance computing cluster at Northern Arizona University, called Monsoon, was used for all evolutionary analyses. Funding. This work was supported by four funding sources: the Technology Research Infrastructure Fund by the Arizona Board of Regents to CH as faculty start-up funds, a training grant to CH and CRi by the Pacific Southwest Center of Excellence in Vector-Borne Diseases funded by the Centers for Disease Control and Prevention (1U01CK000516), a New Investigator Award (ADHS18-198866) to CH from the Arizona Biomedical Research Center, and a Bridge-Funding Initiative Award from the Flinn Foundation to CH.
Funding Information:
This work was supported by four funding sources: the Technology Research Infrastructure Fund by the Arizona Board of Regents to CH as faculty start-up funds, a training grant to CH and CRi by the Pacific Southwest Center of Excellence in Vector-Borne Diseases funded by the Centers for Disease Control and Prevention (1U01CK000516), a New Investigator Award (ADHS18-198866) to CH from the Arizona Biomedical Research Center, and a Bridge-Funding Initiative Award from the Flinn Foundation to CH.
Publisher Copyright:
© Copyright © 2021 Ridenour, Cocking, Poidmore, Erickson, Brock, Valentine, Roe, Young, Henke, Hung, Wittie, Stefanakos, Sumner, Ruedas, Raman, Seaton, Bendik, Hornstra O’Neill, Sheridan, Centner, Lemmer, Fofanov, Smith, Will, Townsend, Foster, Keim, Engelthaler and Hepp.
PY - 2021/6/8
Y1 - 2021/6/8
N2 - 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.
AB - 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.
KW - BEAST
KW - Culex mosquitoes
KW - St. Louis encephalitis virus
KW - genomics
KW - phylogenetic analysis
UR - http://www.scopus.com/inward/record.url?scp=85108363345&partnerID=8YFLogxK
UR - http://www.scopus.com/inward/citedby.url?scp=85108363345&partnerID=8YFLogxK
U2 - 10.3389/fgene.2021.667895
DO - 10.3389/fgene.2021.667895
M3 - Article
AN - SCOPUS:85108363345
SN - 1664-8021
VL - 12
JO - Frontiers in Genetics
JF - Frontiers in Genetics
M1 - 667895
ER -