Saint Louis Encephalitis - Genetics

Genetics

Five evolutionary genetic studies of SLE virus have been published of which four focused on phylogeny, genetic variation, and recombination dynamics by sequencing the envelope protein gene and parts of other genes.

A recent evolutionary study based on 23 new full open reading frame sequences (near-complete genomes) found that the North American strains belonged to a single clade. Strains were isolated at different points in time (from 1933 to 2001) which allowed for the estimation of divergence times of SLE virus clades and the overall evolutionary rate. Furthermore, this study found an increase in the effective population size of the SLE virus around the end of the 19th century that corresponds to the split of the latest North American clade, suggesting a northwards colonization of SLE virus in the Americas. Scans for natural selection showed that most codons of the SLE virus ORF were evolving neutrally or under negative selection. Positive selection was statistically detected only at on single codon coding for aminoacids belonging to the hypothesized N-linked glycosylation site of the envelope protein. Nevertheless, the latter can be due to selection in vitro (laboratory) rather than in vivo (host). In an independent study 14 out of 106 examined envelope gene sequences were found not to contain a specific codon at position 156 coding for this glycosylation site (Ser→Phe/Tyr).

Another study estimated the evolutionary rate to be 4.1 × 10-4 substitutions/site/year (95% confidence internal 2.5-5.7 × 10-4 ). The virus seems to have evolved in in northern Mexico and then spread northwards with migrating birds.