FIG 2.

Locations of sites under positive selection within the NS5 three-dimensional (3D) structure. The solved structure shows the RdRp structure at the front of the image and the MTase structure behind. The JEV structure follows the standard flavivirus RdRp right-hand conformation consisting of fingers, palm, and thumb characteristic of the flavivirus polymerase. The locations of the four positive-charge changes on the “fingertip” region of the finger subdomain that occur between the GI and GIII NS5 sequences are marked red. Two of these mutations, sites 429 and 432, produce compensatory charge mutations of +1 and −1, respectively. The remaining mutations are marked yellow. See Table 2 and the main text for full details.