Fig. 1.

The phylogeny and genetic diversity of the West Nile virus lineages. A Phylogenetic tree of XJ11129 strains compared with reference strains. Each strain is listed by GenBank accession number, geographic origin, and collection date. Scale bar indicates substitutions per site. Abbreviations of geographic origin are list in Supplementary Table S1. XJ11129 was highlighted with a red solid circle and NY99 was highlighted with a blue solid box. B Pairwise percent identity between nucleotide (lower left) and amino acid (upper right) sequences of the polyprotein. Sequences are labeled in the following format: accession number, 2-letter country code, and year of isolation. C Amino acid differences between XJ11129 and NY99. A total of 23 amino acids were different between these two strains. The numeral subscript after amino acid is the location of each gene.