Figure 2. Sequence phylogeny based on E (envelope) gene nucleotide sequence of Japanese encephalitis virus isolates from pigs and mosquito hosts in Thailand during 2003–2005, with reference to other Southeast Asian isolates. Phylogenetic analysis was performed by using nucleotide alignments, the Kimura 2-parameter algorithm (for the calculation of pairwise distances), and the neighbor-joining method (for tree reconstruction), as implemented in MEGA software (9). The tree was rooted within the Japanese encephalitis serogoup by using Murray Valley virus (GenBank accession nos. E1–51). The robustness of branching patterns was tested by 1,000 bootstrap pseudoreplications. Each strain is abbreviated, followed by the country of origin (and the region of origin in Thailand, e.g., NE = northeast) and year of isolation. Bootstrap values are indicated above the major branch; 33 taxa comprised the ingroup, and all taxa were rooted with Murray Valley virus. A unique gap was treated as a "fifth base." The character state optimization was chosen as accelerated transformation. Consistence index 0.572; retention index 0.7528.