Amino acid sequence alignment of the full-length envelope gene from ROK JEV strains. ROK mosquito pools collected during 2008 and 2010 were aligned with the reference sequences GV (Muar) and GI (K01-JN, K05-GS). Dots indicate consensus. Differences in amino acids between Muar and 10-1827 strains are underlined. Residues enclosed by boxes represent 8 Muar signature amino acids in domain III.