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, and a split from the ancestral South American strains around 1892. 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 one single codon coding for
amino acids 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). ==References==