We analyzed nucleotide sequences from the envelope gene of 11 West Nile (WN
) virus strains collected in New York State during the 2000 transmission se
ason to determine whether they differed genetically from each other and fro
m the initial strain isolated in 1999. The complete envelope genes of these
strains were amplified by reverse transcription-polymerase chain reaction.
The resulting sequences were aligned, the genetic distances were computed,
and a phylogenetic tree was constructed. Ten (0.7%) of 1,503 positions in
the envelope gene were polymorphic in one or more sequences. The genetic di
stances were 0.003 or less. WN virus strains circulating in 2000 were homog
eneous with respect to one another and to a strain isolated in 1999.