West Nile virus (WNV), an arbovirus maintained in a bird-mosquito enzootic 
cycle, can infect other vertebrates including humans. WNV was first reported in 
the US in 1999 where, to date, three genotypes belonging to WNV lineage I have 
been described (NY99, WN02, SW/WN03). We report here the WNV sequences obtained 
from two birds, one mosquito, and 29 selected human samples acquired during the 
US epidemics from 2006-2011 and our examination of the evolutionary dynamics in 
the open-reading frame of WNV isolates reported from 1999-2011. 
Maximum-likelihood and Bayesian methods were used to perform the phylogenetic 
analyses and selection pressure analyses were conducted with the HyPhy package. 
Phylogenetic analysis identified human WNV isolates within the main WNV 
genotypes that have circulated in the US. Within genotype SW/WN03, we have 
identified a cluster with strains derived from blood donors and birds from Idaho 
and North Dakota collected during 2006-2007, termed here MW/WN06. Using 
different codon-based and branch-site selection models, we detected a number of 
codons subjected to positive pressure in WNV genes. The mean nucleotide 
substitution rate for WNV isolates obtained from humans was calculated to be 
5.06×10(-4) substitutions/site/year (s/s/y). The Bayesian skyline plot shows 
that after a period of high genetic variability following the introduction of 
WNV into the US, the WNV population appears to have reached genetic stability. 
The establishment of WNV in the US represents a unique opportunity to understand 
how an arbovirus adapts and evolves in a naïve environment. We describe a novel, 
well-supported cluster of WNV formed by strains collected from humans and birds 
from Idaho and North Dakota. Adequate genetic surveillance is essential to 
public health since new mutants could potentially affect viral pathogenesis, 
decrease performance of diagnostic assays, and negatively impact the efficacy of 
vaccines and the development of specific therapies.