FIG 2.

The nucleotide divergence of SIVmac239 RNA with that of the rhesus macaque correlates with the ability to stimulate IFN-I. (A) Luciferase reporter activity determined in HEK-293T cells cotransfected with SIVmac239 RNA fragments and pISRE-Luc reporter plasmid. (B) Repartition of nucleotide divergence along the SIVmac239 genome. The black line shows the nucleotide divergence of the SIVmac239 genome compared to the macaque rhesus genome, as measured by a chi-square distance in a 500-bp sliding window along the SIVmac239 sequence. Individual contributions of A and C nucleotides to this divergence are shown in black and gray dotted lines, respectively. Nucleotide divergence correlates with luciferase activity (R = 0.36, P < 0.02). White areas indicate regions modified by our optimization algorithm; the limits of the region are reported along the x axis. An SIVmac schematic genome map is presented at the bottom of the figure.