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Previously published WNV isolates used in the analysis included the first WNV isolate from Uganda in 1937 (GenBank accession no. M12294), the Egypt 1951 laboratory strain (Eg101, GenBank accession no. AF260968), and several American isolates, such as the NY 2000-crow3356 isolate.
The sequence of this WNV isolate (TM171-03, submitoed to GenBank under accession no. AY371271) was aligned with all homologous WNV sequences of the same length available from the GenBank library (homologous to nt 466 2,469 in the Flamingo382 strain, GenBank accession no.
A New York WNV isolate (NY WNV) [47], [48] from crow brain was used.
This report is the first of a New World WNV isolate with probable altered E protein glycosylation.
The full-length RNA genome of the WNV isolate from one of the stork-1998 (IS98-ST1) has been sequenced.
WNV primers were based on the New York 1999 WNV isolate (GenBank accession no. AF196835.2) described by Lanciotti et al. (11 ).
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We retained the duplicate sequences (2,206) for our analysis because they reflect the incidence of the corresponding WNV isolates in nature and, further, they do not affect the identification of WNV sequences that are completely (100%) conserved.
In large-scale proteomic analyses such as this study, bias may result from the collection of redundant sequences, derived from identical or highly similar WNV isolates sequenced by surveillance programs.
Together, these data indicated that, although small genetic differences existed in Dallas and Montgomery WNV isolates compared with previous WNV isolates, most changes were unlikely to be adaptive.
Phylogenetic analysis matched these isolates most closely with recent western Mediterranean WNV isolates within lineage 1a.
Moreover, WNV isolates from the northeastern United States occupied the basal position of clade 1.
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