Taxonomically, SLEV is classified within the Japanese encephalitis virus (JEV) complex in the genus Flavivirus of the family Flaviviridae. Related viruses within this group include Japanese encephalitis, Murray Valley encephalitis, West Nile, and Usutu. SLEV consists of a positive-sense, single-stranded RNA enclosed within a capsid composed of a single polypeptide (C) and sur rounded by an envelope containing one glycosylated (E) and one nonglycosylated (M) protein. Marked differences in the severity of SLEV epidemics stimulated interest in possible differences among isolates made over time and space. Detailed studies by the CDC during the 1980s clearly demonstrated geographic variation among 43 different SLEV isolates using oligonucleotide finger printing and virulence in model vertebrate hosts. These strains are grouped into six clusters: (1) east central and Atlantic USA, (2) Florida epidemic, (3) Florida enzootic, (4) eastern USA, (5) Central and South America with mixed virulence, and (6) South America with low virulence. Changes in virulence were attributed, in part, to differences in mosquito vector competence and were supported by the historical presence or absence of human cases. Subsequent genetic sequencing studies extended the understanding of SLEV genetics and provided further insight into patterns of geographical variation. Sequences of the envelope gene from SLEV strains isolated in California from 1952 to 1995 varied temporally and spatially, but indicated regional persistence in the Central Valley for at least 25 years as well as sporadic introduction and extinction. Studies in Texas using a single-strand conformation polymorphism technique showed that multiple SLEV strains circulate concurrently and remain highly focal, whereas other strains amplify and disseminate aggressively during some summers, but then disappear. Further analyses of sequences from 62 isolates made throughout the known geographical range of SLEV indicated that there have been seven lineages that overlapped somewhat with the six groups the CDC defined previously using oligonucleotide fingerprinting: (1) western USA, (2) central and eastern USA and three isolates from Mexico and Central America, (3) one mosquito isolate from Argentina, (4) five isolates from Panama mosquitoes, (5) South American strains plus an isolate from Trinidad, (6) one Panama isolate from a chicken, and (7) two isolates from Argentina rodents. Collectively, these data indicated that SLEV strains vary markedly in virulence and that the frequency and intensity of epidemics in the US may be related to genetic selection by different host systems. Interestingly, transmission within the Neotropics appears to have given rise and/or allowed the persistence of less-virulent strains that rarely amplify to produce epidemic-level transmission, a scenario duplicated by West Nile virus in the Americas.
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