A phylogenetic approach to following West Nile virus in Connecticut

The 1999 outbreak of West Nile (WN) virus in the northeastern United States was the first known natural occurrence of this flavivirus in the Western H emisphere. In 1999 and 2000, 82 independent Connecticut WIN virus isolates were cultured from nine species of birds, five species of mosquitoes, and o ne striped skunk. Nucleotide sequences obtained from these isolates identif ied 30 genetic changes, compared with WN-NY99, in a 921-nt region of the vi ral genome beginning at nucleotide position 205 and ending at 1125. This re gion encodes portions of the nucleocapsid and envelope proteins and include s the entire coding regions for the premembrane and membrane proteins. Amin o acid changes occurred at seven loci in six isolates relative to the WN-NY 99 strain. Although 34 of the isolates showed sequences identical to the WN -NY99 isolate, we were able to show geographical-based clusters of mutation s. In particular, 26 isolates were characterized by mutation of C to T at p osition 858. This group apparently originated in Stamford, CT and dissemina ted to sites located as far as 54 miles from Stamford. Sequences of WIN vir us isolated from both brain and heart tissues from the same avian host were identical in all 14 tested individual birds, suggesting that the mutations we have documented are real and not caused by culture, RNA extraction, or PCR procedures. We conclude that this portion of the viral genome will enab le us to follow the geographical and temporal movement of variant WN virus strains as they adapt to North America.