Posted by Vector and Vector-borne Disease Committee
October 1, 2022
Chase L. Ridenour 1,2, Jill Cocking 1,2, Samuel Poidmore 2, Daryn Erickson 2, Breezy Brock 2, Michael Valentine 3, Chandler C. Roe 1,2, Steven J. Young 4, Jennifer A. Henke 5, Kim Y. Hung 5, Jeremy Wittie 5, Elene Stefanakos 6, Chris Sumner 6, Martha Ruedas 6, Vivek Raman 7, Nicole Seaton 7, William Bendik 7, Heidie M. Hornstra O’Neill 2, Krystal Sheridan 2,3, Heather Centner 3, Darrin Lemmer 3, Viacheslav Fofanov 1,2, Kirk Smith 4, James Will 4, John Townsend 4, Jeffrey T. Foster 2, Paul S. Keim 2,3, David M. Engelthaler 3 and Crystal M. Hepp 1,2*
1 School of Informatics, Computing, and Cyber Systems, Northern Arizona University, Flagstaff, AZ, United States, 2 The Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, AZ, United States, 3 Translational Genomics Research Institute, Flagstaff, AZ, United States, 4 Vector Control Division, Maricopa County Environmental Services Department, Phoenix, AZ, United States, 5 Coachella Valley Mosquito and Vector Control District, Indio, CA, United States, 6 Yuma County Pest Abatement District, Yuma, AZ, United States, 7 Southern Nevada Health District, Las Vegas, NV, United States
- Frontiers in Genetics. 12: 667805 [doi: 10.3389/fgene.2021.667895]
Author’s 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.
Note: This interesting study explored several hypotheses concerning the persistence and movement of SLEV in the SW. Interestingly all recent isolates have been Lineage III previously only known from South America, whereas the historically endemic lineages I and II found only in North America have not been detected since their extinction in 2003 when WNV invaded the SW.