Movement of St. Louis encephalitis virus in the Western United States, 2014- 2018

Abstract

St. Louis encephalitis virus (SLEV) is a flavivirus that circulates in an enzootic cycle between birds and mosquitoes and can also infect humans to cause febrile disease and sometimes encephalitis. Although SLEV is endemic to the United States, no activity was detected in California during the years 2004 through 2014, despite continuous surveillance in mosquitoes and sentinel chickens. In 2015, SLEV-positive mosquito pools were detected in Maricopa County, Arizona, concurrent with an outbreak of human SLEV disease. SLEV-positive mosquito pools were also detected in southeastern California and Nevada in summer 2015. From 2016 to 2018, SLEV was detected in mosquito pools throughout southern and central California, Oregon, Idaho, and Texas. To understand genetic relatedness and geographic dispersal of SLEV in the western United States since 2015, we sequenced four historical genomes (3 from California and 1 from Louisiana) and 26 contemporary SLEV genomes from mosquito pools from locations across the western US. Bayesian phylogeographic approaches were then applied to map the recent spread of SLEV. Three routes of SLEV dispersal in the western United States were identified: Arizona to southern California, Arizona to Central California, and Arizona to all locations east of the Sierra Nevada mountains. Given the topography of the Western United States, these routes may have been limited by mountain ranges that influence the movement of avian reservoirs and mosquito vectors, which probably represents the primary mechanism of SLEV dispersal. Our analysis detected repeated SLEV introductions from Arizona into southern California and limited evidence of year-to-year persistence of genomes of the same ancestry. By contrast, genetic tracing suggests that all SLEV activity since 2015 in central California is the result of a single persistent SLEV introduction. The identification of natural barriers that influence SLEV dispersal enhances our understanding of arbovirus ecology in the western United States and may also support regional public health agencies in implementing more targeted vector mitigation efforts to protect their communities more effectively.

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

“…The 142 genomes we sequenced were genotype III, as they all nested within the Argentinian samples ( Supplementary Figure S1 ). Swetnam et al (2020) sequenced 30 SLEV genomes from the Southwestern United States sampled from 2015 to 2018 and similarly found them to be genotype III. Therefore, our results corroborate Swetnam et al (2020) along with previous work by White et al (2016) and Diaz et al (2018) .…”

“…The Maricopa County sister clade is composed of a single 2015 and several 2017, 2018, and 2019 samples. Each year is nested within the previous year, indicating that SLEV has become endemic in Maricopa County, as it has in central and northern California ( Swetnam et al, 2020 ). The formation of polytomies within each year is most likely the result of oversampling as described for clade 1.…”

Epidemiologic and environmental characterization of the Re-emergence of St. Louis Encephalitis Virus in California, 2015–2020

“…Though SLEV was known to overwinter in the Salton Sea area [ 52 , 53 ] and persisted in the Central Valley for at least 25 concurrent years, genomic tracing from different sites in California prior to 2003 indicated periodic extinction and reintroduction of the virus into the state [ 3 , 54 ], similar to the apparent pattern since 2015, although SLEV’s apparent absences were shorter in prior decades. Since the re-emergence of SLEV in 2015, phylogeographic analyses indicated that repeated introductions of SLEV from Arizona into Southern California, without year-to-year persistence of the same viral strains [ 55 ]. Within Central California, continual SLEV activity since 2016 was likely the result of a single SLEV introduction that has persisted [ 55 ].…”

Updated distribution maps of predominant Culex mosquitoes across the Americas

“…Disease outbreaks facilitated by Culex species are increasing in frequency, and these mosquitoes will continue to be important vectors for emergent and re-emerging diseases [ 7 – 9 ]. For example, outbreaks of EEEV occurred in multiple states within the USA in summer 2019, which resulted in 34 infections and 11 deaths [ 10 ].…”

“…In parallel to expanding mosquito species distributions, several mosquito-borne viruses are expanding as well, impacting novel and susceptible human populations [ 9 , 18 , 25 ]. For example, since 2014, specific strains of SLEV thought to be restricted to Argentina have been reported in Arizona and California [ 9 , 26 ]. There has also been an increased risk for WNV in Canada, both in urban and rural areas [ 27 ].…”