Evolutionary Dynamics of West Nile Virus in the United States, 1999–2011: Phylogeny, Selection Pressure and Evolutionary Time-Scale Analysis

Abstract

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.

Terrestrial Bird Migration and West Nile Virus Circulation, United States

“…We used the GTR+Γ+I (general time reversible with gamma rate distribution and invariable sites) model to infer nucleotide substitution frequencies, an uncorrelated lognormal clock model to infer the mutation rate, and a Bayesian Skyline tree prior to model changes in population size. The evolution rate mean was restricted to 10 −4 through 9 × 10 −4 substitutions/site/year, consistent with previously reported rates for WNV evolution ( 7 , 33 ). …”

“…Since then, phylogeographic studies have reported frequent mixing of WNV strains from local and distant locations. The most notable exception is California , where several genetic studies have shown limited movement into and out of the state ( 6 , 7 ). …”

Fluid Spatial Dynamics of West Nile Virus in the United States: Rapid Spread in a Permissive Host Environment

“…Previous studies of the molecular evolution of WNV in North America have largely utilized sequences from mosquitoes, been restricted to local areas, relied on partial genomes (18,26,46,47,50), or mainly focused on those viruses sampled from humans within the context of WNV in birds (23). Hence, the current study is notable in that we obtained ϳ300 complete genome sequences of WNV from birds across the United States.…”

“…Hence, we reasoned that although small in number, the inclusion of these sequences could bias estimates of evolutionary rate. In addition, it has previously been shown that human sequences fall at multiple places across the WNV phylogeny (23). Sequence alignment was performed using MAFFT (32), and these results were inspected manually.…”

“…WNV phylogenies are also characterized by relatively little spatial structure (18,22,23), although a relatively large clade of mosquito WNV sequences was recently documented in California (24). In addition, birds seem to harbor greater WNV diversity than mosquitoes (25,26).…”