Abstract
St. Louis encephalitis virus (SLEV) has been regularly isolated throughout the Americas since 1933. Previous phylogenetic studies involving 62 isolates have defined seven major lineages (I–VII), further divided into 14 clades. In this study, 28 strains isolated in Texas in 1991 and 2001–2003, and three older, previously unsequenced strains from Jamaica and California were sequenced over the envelope protein gene. The inclusion of these new sequences, and others published since 2001, has allowed better delineation of the previously published SLEV lineages, in particular the clades of lineage II. Phylogenetic analysis of 106 isolates identified 13 clades. All 1991 and 2001–2003 isolates from Nueces, Jefferson and Harris Counties (Texas Gulf Coast) group in clade IIB with other isolates from these counties isolated during the 1980s and 1990s. This lack of evidence for introduction of novel strains into the Texas Gulf Coast over a long period of time is consistent with overwintering of SLEV in this region. Two El Paso isolates, both from 2002, group in clade VA with recent Californian isolates from 1998–2001 and some South American strains with a broad temporal range. Overall, these data are consistent with multiple introductions of SLEV from South America into North America, and provide support for the hypothesis that in most situations, SLEV circulates within a locality, with occasional incursions from other areas. Finally, SLEV has much lower nucleotide (10.1 %) and amino acid variation (2.8 %) than other members of the Japanese encephalitis virus complex (maximum variation 24.6 % nucleotide and 11.8 % amino acid).
Highlights
The current study investigated the genetic relationships of a number of recent isolates from Texas, some older isolates from California and one from Jamaica, with previously studied isolates and proposes an updated classification of some St. Louis encephalitis virus (SLEV) clades
Twenty-eight new isolates and 78 sequences from GenBank were included in this study; in total 106 E gene sequences were analysed
We lack statistical evidence to draw specific conclusions regarding the lack of SLEV isolates in those years, it is interesting to note that the paucity of SLEV isolates has been seen following the introduction of WNV into this area
Summary
There is some evidence to suggest spread of individual variants across the USA, as in the case of the 1975 epidemic, with isolates from Tennessee, Mississippi and California grouping together (Kramer & Chandler, 2001) and variation of genotype within a single geographical location (Kramer et al, 1997; Reisen et al, 2002). Since the introduction of WNV into southern California, no SLEV isolates have been detected despite substantial surveillance of mosquito populations (Fang & Reisen, 2006), suggesting that these viruses may not be able to coexist when sharing the same mosquito vector. Amino acid variation in the E protein was found to be very limited compared with variation between strains of other viruses in the JE complex
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