Emerging Infectious Diseases - Vol. 14, No. 2, February 2008 by Centers for Disease Control and Prevention

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Emerg Infect Dis. 2004;10:2221–4. Coia G, Parker MD, Speight G, Byrne ME, Westaway EG. Nucleotide and complete amino acid sequences of Kunjin virus: definitive gene order and characteristics of the virus-specified protein. J Gen Virol. 1988;69:1–21. Lanciotti RS, Roehrig JT, Deubel V, Smith J, Parker M, Steele K, et al. Origin of the West Nile virus responsible for an outbreak of encephalitis in the northeastern United States. Science. 1999;286: 2333–7. Smithburn KC, Hughes TP, Burke AV, Paul JH.

The 2 strains from North America, New York (NY385–99) and Mexico (TM171–03), were similarly conserved. In contrast, the Madagascar strain, AnMg798, differed by >3% at the amino acid level from all lineage 2 strains from South Africa or Uganda B956D117B3, and the Few amino acid differences were observed between the structural proteins of the South African strains (Figure 2). SA381/00 had only 1 difference in the premembrane (prM) protein at position 105 relative to the highly neuroinvasive strains (Ala105Val) (Figure 2).

SA93/01 and SPU116/89 clustered together; H442 and SA381/00 were on separate branches within lineage 2 with respect to the full genome sequences or with respect to individual E, NS3, and NS5 genes (data not shown). Although the Indian strain clustered with lineage 1, p-distance analysis suggested that it was as distant to the lineage 1 strains (20% differences) as to the lineage 2 strains (21%–22%) relative to <5% differences within lineage 1C and 12% differences between 1A and 1B. It was therefore termed lineage 5, as suggested by Bondre et al.

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